Porcine polymorphisms and methods for detecting them

ABSTRACT

Identification of a pig as resistant or non-resistant to enterotoxigenic  E. Coli  (ETEC). Particularly, there is provided methods, probes and DNA molecules involved in identifying a pig as resistant or non-resistant to ETEC. There is also provided methods for breeding pigs using the information of resistance/non-resistance, mixed boar semen, and methods for developing drugs to compensate for non-resistance to ETEC.

FIELD OF THE INVENTION

The present invention relates in its broadest aspect to identification of a pig as resistant or non-resistant to enterotoxigenic E. coli (ETEC). Particularly, there is provided methods, probes and DNA molecules involved in identifying a pig as resistant or non-resistant to ETEC. The present invention further relates to methods for breeding pigs using the information of resistance/non-resistance, mixed boar semen, and methods for developing drugs to compensate for non-resistance to ETEC.

TECHNICAL BACKGROUND AND PRIOR ART

In breeding of pigs a major problem is to keep the new-born, and in particular post weaning young pigs, disease-free. In that respect intestinal disorders are among the most widespread and serious problems, and swine breeding and production farms all over the world suffer sizeable losses of livestock each year from outbreak of these diseases. Further losses arise from the costs of medication, growth retardation and other consequences of the diseases, which may be more substantial than direct damage due to mortality.

It is known that the causative agents responsible for a significant number of the diarrhoeas in young pigs are enterotoxigenic strains of E. coli ETEC. Several ETEC have been isolated from infected animals and types of E. coli strains, such as E. coli F18, and E. coli F4 (formerly known as K88), are among the major lethal strains found in young pigs.

The designations F18 and F4 refer to fimbriae types of the ETEC and are used to distinguished the different strains. The adhesive fimbriae mediate the colonisation of E. coli in the intestine. Colonisation depends on the adherence of the bacteria to the enterocytes and subsequent proliferation and toxin production of the ETEC will cause the diarrhoea.

The disease develops after the ETECs are introduced into the intestinal tract of the piglets. The ETEC bacteria adhere to the wall of the small intestine through their surface protein antigens (fimbriae), multiply there in large numbers and transfer their toxins directly to the intestinal epithelial cells. Due to the effect exerted by the toxins, the fluid-absorbing activity of intestinal epithelial cells will cease and the cells will secrete a large volume of fluid into the intestinal lumen resulting in the development of more or less severe diarrhoeas.

In the art, efforts have been made in order to control diarrhoea in animals, such as pigs, caused by ETEC. U.S. Pat. No. 4,443,549 describes a method of producing monoclonal antibodies against adhesion of a pathogenic bacterium, which adhesion mediates attachment of the bacterium to mucocutaneous tissue. The antibodies may be used in a pharmaceutical composition suitable for oral administration to animals.

U.S. Pat. No. 4,761,372 discloses a plasmid comprising genes coding for an immunogenic, non-toxic, heat labile enterotoxin and/or a non-toxic, heat stable enterotoxin and an E. coli containing this plasmid for use as a live vaccine for vaccinating humans and animals against diarrheal diseases.

Additionally, WO 00/58476 describes a method of producing a live, orally applicable E. coli vaccine for the prevention of postweaning diarrhoea in pigs. An enterotoxin-free strain of E. coli which produces two adhesive fimbriae (F4 and F18) are administered to the young pigs in an attempt to provide local protection.

However, not all pigs succumb to E. coli infections. Susceptibility to adhesion, i.e. expression of receptors in pigs for binding of particular fimbriae, has been shown to be genetically controlled by the host. The mechanism for resistance appears to be that intestinal borders in resistant animals are not colonised by E. coli i.e., the bacteria do not adhere to the intestinal walls of resistant animals.

An attempt to detect E. coli resistance is reported in WO 98/53101. The application relates to a method for differentiating between pigs that are either resistant or susceptible to F18 E. coli related diseases. The differentiation is performed using a DNA test for DNA polymorphisms in the alpha (1,2) fucosyltransferase 1 (FUT1) gene on the porcine chromosome 6.

Enterotoxigenic Escherichia coli cells (ETEC) that expresses the F4ab or F4ac fimbriae (formerly know as K88ab and K88ac) are major causes of diarrhoea and death in neonatal and young pigs (Wilson and Francis, 1986). In Denmark, ETEC F4 is present in about 25% of the reported diarrhoea cases (Ojeniyi et al., 1994).

In 1975 Sellwood and co-workers published a paper describing the existence of two pig phenotypes in relation to ETEC F4, namely resistant pigs and susceptible pigs, respectively. In 1977, Gibbons et al. showed that ETEC F4ac resistance was inherited as an autosomal recessive Mendelian trait and linkage to the transferrin locus (TF) was suggested and later confirmed (Guérin et al. 1993). Linkage mapping of the porcine loci responsible for susceptibility towards ETEC F4ac and F4ab led to the hypothesis that a potential candidate gene was located on pig chromosome 13 (Edfors-Lilja et al., 1995), but no candidate gene was found or suggested. This means that the only available diagnostic test for this type of ETEC F4 resistance is the adhesion test developed by Sellwood et al. in 1975. Since the adhesion test either demands major intestinal surgery or slaughter of the pig and the fact that it is very laborious makes it difficult to incorporate it into breeding programs.

The prerequisites that need to be fulfilled in order to incorporate a diagnostic test into a breeding program is that it needs to be quick, easy to use and allowing precise genotyping of live animals; however, so far no suitable method fulfils this need.

SUMMARY OF THE INVENTION

The present invention relates to the applications of newly discovered genetic. polymorphisms linked to resistance to E. coli and located in the region between and including the markers SW2196 and SW225 on the porcine chromosome (SSC) 13.

Some of the advantages of the present invention include ease of use, non-invasive testing and fast test result. Seen from a broader perspective the advantages of the various aspects of the present invention are e.g. an environmentally safer meat production with a reduced consumption of antibiotics, better economy of the meat production and healthier animals in the production.

Accordingly, in a first aspect the present invention pertains to an isolated nucleic acid (NA) molecule, comprising an allele of a genetic polymorphism linked to resistance to enterotoxigenic E. coli (ETEC), said genetic polymorphism being located in the region between and including the markers SW2196 and SW225 on the porcine chromosome 13.

Another aspect of the invention provides a NA probe, which comprises a NA sequence that is homologous to a fragment of the above NA molecule.

Yet another aspect of the present invention relates to a method for identifying if a pig is resistance to ETEC, the method comprising:

-   i) obtaining a sample from said pig, said sample comprising genetic     material, -   ii) determining by use of said sample if the pig is homozygous for     an allele of a genetic polymorphism linked to resistance to ETEC,     said genetic polymorphism being located in the region between and     including the markers SW2196 and SW225 on the porcine chromosome 13,     and -   iii) identifying the pig as resistant to ETEC if the pig is     homozygous for the allele of genetic polymorphism linked to     resistance.

A further aspect of the present invention relates to the use of the isolated NA molecule and/or the NA probe, as a probe for detecting a porcine allele of a genetic polymorphism linked to resistant to ETEC.

Still another aspect of the present invention relates to the use of a pair of NA molecules for primers in a PCR-based method, said PCR-based method being used in a method for identifying whether a pig is resistant or non-resistant to ETEC, said pair of NA molecules being selected from the group consisting of SEQ ID NO: 18 and SEQ ID NO: 19, SEQ ID NO: 20 and SEQ ID NO: 21, SEQ ID NO: 22 and SEQ ID NO: 23, SEQ ID NO: 24 and SEQ ID NO: 25, SEQ ID NO: 26 and SEQ ID NO: 27, SEQ ID NO: 28 and SEQ ID NO: 29, SEQ ID NO: 30 and SEQ ID NO: 31, SEQ ID NO: 32 and SEQ ID NO: 33, SEQ ID NO: 34 and SEQ ID NO: 35, SEQ ID NO: 36 and SEQ ID NO: 37, SEQ ID NO: 38 and SEQ ID NO: 39, SEQ ID NO: 40 and SEQ ID NO: 41, SEQ ID NO: 42 and SEQ ID NO: 43, SEQ ID NO: 44 and SEQ ID NO: 45, SEQ ID NO: 46 and SEQ ID NO: 47, SEQ ID NO: 48 and SEQ ID NO: 49, SEQ ID NO: 50 and SEQ ID NO: 51, SEQ ID NO: 52 and SEQ ID NO: 53, SEQ ID NO: 54 and SEQ ID NO: 55, SEQ ID NO: 56 and SEQ ID NO: 57, SEQ ID NO: 58 and SEQ ID NO: 59, SEQ ID NO: 60 and SEQ ID NO: 61, SEQ ID NO: 62 and SEQ ID NO: 63, SEQ ID NO: 64 and SEQ ID NO: 65 and their complementary sequences.

Another aspect of the present invention provides a kit for determining if a pig is homozygous, heterozygous or non-carrier of an allele of a genetic polymorphism being linked to resistance to ETEC, said kit comprising a first component selected from the group consisting of a NA probe, a NA molecule, a pair of PCR-primers, a restriction enzyme and any combination thereof.

Yet another aspect of the present invention relates to a method for breeding pigs that are resistant to ETEC, the method comprising

-   i) selecting a first pig, said pig identified as resistant to ETEC     using the method described herein; and -   ii) breeding said first pig with a second pig, to obtain a pig     progeny that is more resistant to ETEC than progeny from randomly     chosen parent pigs.

In a still further aspect, the invention provides an isolated NA molecules for the use as an antisense-NA, a iRNA, a Ribosyme, an ETC for genetic medicine, gene therapy or cinetoplastic DNA repair.

The present invention also pertains to a method for producing pork meat, the method comprising i) obtaining a pig progeny as defined herein, and ii) preparing pork meat from the pig progeny.

In one interesting aspect, the invention relates to a method for screening a potential drug candidate for treatment of non-resistance to ETEC, the method comprising

-   i) selecting a test population of pigs that are identified as     non-resistant to ETEC, said identification being performed using the     method described herein; -   ii) administering the potential drug candidate to the test     population, and -   iii) evaluation the efficacy of the potential drug candidate on the     test population.

In a further aspect, the present invention provides a mixed boar semen, comprising semen from at least two boars, said boars being identified as resistant to ETEC using the method described herein.

DETAILED DESCRIPTION OF THE INVENTION DEFINITIONS

The term “nucleic acid molecule” or “NA molecule” refers in the present context to an oligomer or polymer of ribonucleic acid (RNA) or deoxyribonucleic acid (DNA) or mimetics thereof. This term includes molecules composed of naturally-occurring nucleobases, sugars and covalent internucleoside (backbone) linkages as well as molecules having non-naturally occurring nucleobases, sugars and covalent internucleoside (backbone) linkages which function similarly or combinations thereof. Such modified or substituted nucleic acids are often preferred over native forms because of desirable properties such as, for example, enhanced cellular uptake, enhanced affinity for nucleic acid target and increased stability in the presence of nucleases and other enzymes, and are in the present context described by the terms “nucleic acid analogues” or “nucleic acid mimics”. Preferred examples of nucleic acid mimetics are peptide nucleic acid (PNA-), Locked Nucleic Acid (LNA-), xylo-LNA-, phosphorothioate-, 2′-methoxy-, 2′-methoxyethoxy-, morpholino- and phosphoramidate-containing molecules or the like.

As used herein, the term “ETEC” refers to bacteria from genus Escherichia and species Escherichia coli which are enterotoxigenic and/or enteropathogenic E. coli (ETEC) bacteria. The ETEC are distinguished by their fimbriae type and the ETEC group includes but are not limited to E. coli F4 (formerly known as K88) such as E. coli F4ab/F4ac, E. coli F4ab, E. coli F4ac, E. coli F4ad, E. coli 0149, E. coli F5 (formerly known as K99), E. coli F6 (formerly known as 987P), E. coli F41, E. coli F18, E. coli F18ab, E. coli F107, F18ac, E. coli 2134P, E. coli Av24, and any combinations thereof.

The term “allele of the genetic polymorphism linked to resistance to ETEC” relates to the NA sequence that is observed in connection with resistance to ETEC and the term “allele of the genetic polymorphism linked to non-resistance to ETEC” is a nucleotide sequence that is observed in connection with non-resistance to ETEC.

The term “NA sequence” may be employed to designate a nucleic acid molecule. More precisely, the expression “NA sequence” encompasses the nucleic material itself and is thus not restricted to the sequence information (i.e. the succession of letters chosen among the four bases) that biochemically characterises a specific DNA or RNA molecule.

The term “homology” indicates a quantitative measure of the degree of homology between two amino acid sequences of equal length or between two nucleotide sequences of equal length. If the two sequences to be compared are not of equal length, they must be aligned to the best possible fit. The sequence identity can be calculated as ((Nref−Ndif)100)/(Nref), wherein Ndif is the total number of non-identical residues in the two sequences when aligned, and wherein Nref is the number of residues in one of the sequences. Hence, the DNA sequence AGTCAGTC will have a sequence identity of 75% with the sequence AATCAATC (Ndif=2 and Nref=8). A gap is counted as nonidentity of the specific residue(s), i.e. the DNA sequence AGTGTC will have a sequence identity of 75% with the DNA sequence AGTCAGTC (Ndif=2 and Nref=8). Sequence identity can alternatively be calculated by the BLAST program, e.g. the BLASTP program (Pearson & Lipman (1988), available at the NCBI webpage. In one embodiment of the invention, alignment is performed with the global align algorithm with default parameters as described by Huang & Miller (1991).

The term “homologous” means that one single-stranded nucleic acid sequence may hybridise to a complementary single-stranded nucleic acid sequence. The degree of hybridisation may depend on a number of factors including the amount of identity between the sequences and the hybridisation conditions such as temperature and salt concentration.

The term “lod score” has the following meaning: In order to determine if an allele of genetic polymorphism is linked to resistance to ETEC, a lod score can be applied. A lod score, which is also sometimes referred to as Z_(max), indicates the probability (the logarithm of the ratio of the likelihood) that a genetic marker locus and a specific gene locus are linked at a particular distance. Lod scores may e.g. be calculated by applying a computer programme such as the MLINK programme of the UNKAGE package (Lathrop et al., 1985). A lod score greater than 3.0 is considered to be significant evidence for linkage between the genetic polymorphism and the resistance to ETEC or gene locus.

The term “fragment” relates to a subset of larger NA molecule, wherein said subset comprises at least 10 nucleotides, such as at least 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250, 300, 400, 500, 1000, 2000, 5000 such as at least 10000 nucleotides. When a fragment of a NA molecule is used as a primer for a PCR-based method it is preferred that the subset comprises from 10-30 nucleotides and even more preferred from 15-23 nucleotides, such as 15, 16, 17, 18, 19, 20, 21, 22 or 23 nucleotides.

The term “genetic polymorphism” relates to a variable nucleotide sequence (polymorphic) that may be present in porcine genomic DNA on a chromosome. Genetic polymorphisms include polymorphisms selected from the group consisting of a single nucleotide polymorphism (SNP), a variable number tandem repeat polymorphism, an interspersed repetitive DNA, insertions, duplications, deletions, amplifications, rearrangements, a combination of SNP's, short tandem repeats, dinucleotide repeats, interspersed repetitive DNA and any combination of these. Variable nucleotide sequence may e.g. be distinguishable by nucleic acid amplification and observation of a difference in size or sequence of nucleotides due to the polymorphism.

The term “pig” comprises all members of the family Suidae species Sus scrofa. Today a large number of relatively well characterised breeds of pigs exists and many of these breeds are susceptible to variable degrees to enterotoxigenic or enteropathogenic E. coli strains. It is evident that a method according to present invention wherein the pig is selected from the group of pigs consisting of a descender of Sus scrofa could result in a breed wherein the animals were resistant to ETEC. At present, there are 10 breeds of swine, which are recognised and can be registered as pure-bred in the United States. These are Berkshire, Chester White, Duroc, Hampshire, Landrace, Poland China, Spot, Yorkshire, Hereford and Tamworth.

In the highly industrialised animal production of today four breeds being Landrace, Yorkshire, Duroc and Hampshire are particular important. Individuals from all four breeds may be non-resistant to ETEC and all populations could benefit from a breeding programme comprising the method disclosed in the present invention.

Other examples of pig breeds are Landrace, Hampshire, Duroc, Yorkshire, Danish Yorkshire, Danish Duroc, Landrace, Danish Landrace, White Danish Landrace, Blackspotted (Sortbroget) Danish Landrace, Hampshire, Danish Hampshire, Poland China, Hereford American Landrace, American Yorkshire, Arapawa Island, Ba Xuyen, Bantu, Bazna, Beijing Black, Belarus Black Pied, Belgian Landrace, Berkshire, British Landrace, British Lop, Bulgarian White, Cantonese, Chester White, Czech Improved White, Dermantsi Pied, Dutch Landrace, Fengjing, Finnish Landrace, French Landrace, German Landrace, Gloucestershire Old Spots, Guinea Hog, Hezuo, Iberian, Italian Landrace, Jinhua, Kele, Krskopolje, Kunekune, Lacombe, Large Black, Large Black-white, Large White, Lithuanian Native, Meishan, Middle White, Minzhu, Mong Cai, Mukota, Mora Romagnola, Moura, Mulefoot, Neijiang, Ningxiang, Norwegian Landrace, Ossabaw Island, Oxford Sandy and Black, Philippine Native, Pietrain, Red Wattle, Saddleback, Spots, Swedish Landrace, Swallow Belied Mangalitza, Tamworth, Thuoc Nhieu, Tibetan, Turopoije, Vietnamese Potbelly, Welsh and Wuzhishan.

It should further be noted that the method of the present invention may be used to identify resistant animals from any crossbreeding of any of the pig families and breeds mentioned above.

The term “genetic material” should in the present context be interpreted in its broadest aspect and may comprise one or more components selected from the group consisting of genomic DNA, such as chromosomes, mRNA, and fragments and/or digests of these molecules.

The term “genomic DNA” should be interpreted in its broadest aspect and may comprise one or more components selected from the group consisting of genomic DNA, such as chromosomes, and fragments and/or digests of these molecules.

DESCRIPTION

It should be emphasised that all terms, embodiments and features described herein may be used with all of the aspects mentioned herein.

In a first aspect of the present invention there is provided an isolated nucleic acid (NA) molecule, comprising an allele of a genetic polymorphism linked to resistance to enterotoxigenic E. coli (ETEC), said genetic polymorphism being located in the region between and including the markers SW2196 and SW225 on the porcine chromosome 13. In an useful embodiment, the genetic polymorphism is located in the region flanked by and including the markers SW207 and S0075.

In one embodiment of the present invention, the allele of a genetic polymorphism linked to resistance to ETEC renders a pig, which is homozygous with respect to said allele, resistant to ETEC.

In one embodiment of the present invention, a pig which is homozygous with respect to said allele of a genetic polymorphism linked to resistance to ETEC, is resistant to ETEC.

In a preferred embodiment of the present invention, the ETEC is E. coli F4 and/or E. coli F4 ab/ac.

In preferred embodiments, the isolated NA molecule may comprise an allele of the genetic polymorphism that is linked to resistance to ETEC with a lod score of at least 3.0 including at least 4.0, 5.0, 6.0, 7.0, 8.0 or 9.0, 10 such as at least 50.

In a preferred embodiment of the invention, the isolated NA molecule comprises an allele of the genetic polymorphism that is linked to resistance to ETEC. The isolated NA molecule may also comprise a NA sequence, which is located in the porcine MUC4 gene.

In certain preferred embodiments of the present invention, the isolated NA molecule comprises a NA sequence which is identical or has at least 90% homology, such as at least 95% or at least 99% homology to a sequence selected from the group of sequences consisting of SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 13, SEQ ID NO: 14, SEQ ID NO: 15, SEQ ID NO: 16, SEQ ID NO: 17, SEQ ID NO: 67, SEQ ID NO: 68, SEQ ID NO: 81, SEQ ID NO: 82, SEQ ID NO: 83, SEQ ID NO: 84, SEQ ID NO: 85, SEQ ID NO: 86, SEQ ID NO: 87, SEQ ID NO: 88, SEQ ID NO: 89, SEQ ID NO: 90, SEQ ID NO: 91, SEQ ID NO: 92, SEQ ID NO: 93, SEQ ID NO: 94, SEQ ID NO: 95, SEQ ID NO: 96, SEQ ID NO: 97, SEQ ID NO: 98, SEQ ID NO: 99, SEQ ID NO: 100, SEQ ID NO: 101, SEQ ID NO: 102, SEQ ID NO: 103, SEQ ID NO: 104, SEQ ID NO: 105, SEQ ID NO: 106, SEQ ID NO: 107, SEQ ID NO: 108, SEQ ID NO: 109, SEQ ID NO: 110, SEQ ID NO: 111, SEQ ID NO: 112, SEQ ID NO: 113, SEQ ID NO: 114, SEQ ID NO: 115, SEQ ID NO: 116, SEQ ID NO: 117, SEQ ID NO: 118, SEQ ID NO: 119, SEQ ID NO: 120, SEQ ID NO: 121, SEQ ID NO: 122, SEQ ID NO: 123, SEQ ID NO: 124, SEQ ID NO: 125, SEQ ID NO: 126, SEQ ID NO: 127, SEQ ID NO: 128, SEQ ID NO: 129, SEQ ID NO: 130, SEQ ID NO: 131, SEQ ID NO: 132, SEQ ID NO: 133, SEQ ID NO: 134, SEQ ID NO: 135, SEQ ID NO: 136, SEQ ID NO: 137, SEQ ID NO: 138, SEQ ID NO: 139, SEQ ID NO: 140, SEQ ID NO: 141, SEQ ID NO: 142, SEQ ID NO: 143, SEQ ID NO: 144, SEQ ID NO: 145, SEQ ID NO: 146, SEQ ID NO: 147, SEQ ID NO: 148, SEQ ID NO: 149, SEQ ID NO: 150, SEQ ID NO: 151, SEQ ID NO: 152, SEQ ID NO: 153, SEQ ID NO: 154, SEQ ID NO: 155, SEQ ID NO: 156, SEQ ID NO: 157, SEQ ID NO: 158, SEQ ID NO: 159, SEQ ID NO: 160, SEQ ID NO: 161, SEQ ID NO: 162, SEQ ID NO: 163, SEQ ID NO: 164, SEQ ID NO: 165, SEQ ID NO: 166, SEQ ID NO: 167, SEQ ID NO: 168, SEQ ID NO: 169, SEQ ID NO: 170, SEQ ID NO: 171, SEQ ID NO: 172, SEQ ID NO: 173, SEQ ID NO: 174, SEQ ID NO: 175, SEQ ID NO: 176, SEQ ID NO: 177, SEQ ID NO: 178, SEQ ID NO: 179, SEQ ID NO: 180, SEQ ID NO: 181, SEQ ID NO: 182, SEQ ID NO: 183, SEQ ID NO: 184, SEQ ID NO: 185, SEQ ID NO: 186, SEQ ID NO: 187, SEQ ID NO: 188, SEQ ID NO: 189, SEQ ID NO: 190, SEQ ID NO: 191, SEQ ID NO: 192, SEQ ID NO: 193, SEQ ID NO: 194, SEQ ID NO: 195, SEQ ID NO: 196, SEQ ID NO: 197, their complementary sequences and any fragments thereof.

In further preferred embodiments of the present invention, the isolated NA molecule comprises a NA sequence which is identical or has at least 90% homology, such as at least 95% or 99% homology to a sequence selected from the group of sequences consisting of SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 13, SEQ ID NO: 14, SEQ ID NO: 15, SEQ ID NO: 16, SEQ ID NO: 17, SEQ ID NO: 67, SEQ ID NO: 68, SEQ ID NO: 81, SEQ ID NO: 82, SEQ ID NO: 83, SEQ ID NO: 84, SEQ ID NO: 85, SEQ ID NO: 86, SEQ ID NO: 87, SEQ ID NO: 88, SEQ ID NO: 5 89, SEQ ID NO: 90, SEQ ID NO: 91, SEQ ID NO: 92, SEQ ID NO: 93, SEQ ID NO: 94, SEQ ID NO: 95, SEQ ID NO: 96, SEQ ID NO: 97, SEQ ID NO: 98, SEQ ID NO: 99, SEQ ID NO: 100, SEQ ID NO: 101, their complementary sequences and fragments thereof.

In an especially preferred embodiment of the present invention, the isolated NA molecule comprises a NA sequence which is identical or has at least 90% homology, such as at least 95% or 99% homology to a sequence selected from the group of sequences consisting of SEQ ID NO: 6, SEQ ID NO: 8, SEQ ID NO: 82, SEQ ID NO: 83, SEQ ID NO: 87 and SEQ ID NO: 88, their complementary sequences and fragments thereof.

In a suitable embodiment, the isolated NA molecule comprises a NA sequence that distinguishes pigs, which are resistant to ETEC from pigs, which are non-resistant to ETEC.

In another embodiment of the present invention, the isolated NA molecule is a NA molecule, which is in complete or nearly complete linkage disequilibrium with any of the NA molecules described above.

Alleles at two or more neighbouring loci show linkage disequilibrium when they occur together in frequencies significantly different from those predicted from the individual allele frequencies. Complete linkage disequilibrium generally occurs when two NA sequences (e.g. a genetic polymorphism and the porcine MUC4 gene) are physically very close to each other on the chromosome and where the opportunities for recombination have been limited. Where the two NA sequences are in linkage equilibrium then it is essential to determine the linkage phase (i.e. how the alleles are associated) in each pedigree before the markers can be used to predict genotypes at the gene of interest. Genetic polymorphisms that are In partial, but not complete, linkage disequilibrium with the gene of interest may have some utility in predictive tests.

In a preferred embodiment of the invention, the NA molecule comprise a site for a genetic polymorphism such as e.g. A1059G in SEQ ID NO: 6, T1125G in SEQ ID NO: 6, A1134G in SEQ ID NO: 6, C1138G in SEQ ID NO: 6, C1849G in SEQ ID NO: 8, C2129T in SEQ ID NO: 8, A4847G in SEQ ID NO: 82, T4913G in SEQ ID NO: 82, A4922G in SEQ ID NO: 82, C4926G in SEQ ID NO: 82, A1659T in SEQ ID NO: 83, T1666G in SEQ ID NO: 83, C1684A in SEQ ID NO: 83, T1740A in SEQ ID NO: 83, C1795T in SEQ ID NO: 83, T1820G in SEQ ID NO: 83, C1912T in SEQ ID NO: 83, G2997A in SEQ ID NO: 83, G3277C in SEQ ID NO: 83 or any of their complementary sequences.

The NA molecule may be selected so as to comprise a site for genetic polymorphism such as the variation found at position 1726 of SEQ ID NO: 83 where the nucleotides 10 AACGTG in are present in a resistant pig and a 6 basepair deletion is observed in an ETEC susceptible pig; the variation found at position 2009 of SEQ ID NO: 83, where pigs either dislay a T or a deletion of the T; the variation found at position 332 of SEQ ID NO: 87, where a SNP shifting between G and A is present; or the variation found at position 3530 of SEQ ID NO: 88, where a SNP shifting between G and 15 A is present. Without being bound by theory, these three genetic polymorphisms are believed to be associated to resistance ETEC.

The invention provides in a second aspect a NA probe, which comprises a NA sequence that is homologous to a fragment of an isolated NA molecule as described above.

The NA probe may be specific for an allele of at least one SNP selected from the group of SNPs consisting of A1059G in SEQ ID NO: 6, T1125G in SEQ ID NO: 6, A1134G in SEQ ID NO: 6, C1138G in SEQ ID NO: 6, C1849G in SEQ ID NO: 8, C2129T in SEQ ID NO: 8, A4847G in SEQ ID NO: 82, T4913G in SEQ ID NO: 82, A4922G in SEQ ID NO: 82, C4926G in SEQ ID NO: 82, A1659T in SEQ ID NO: 83, T1666G in SEQ ID NO: 83, C1684A in SEQ ID NO: 83, T1740A in SEQ ID NO: 83, C1795T in SEQ ID NO: 83, T1820G in SEQ ID NO: 83, C1912T in SEQ ID NO: 83, G2997A in SEQ ID NO: 83, 30 G3277C in SEQ ID NO: 83 and their complementary sequences.

A NA probe may be specific for an allele of at least one genetic polymorphism comprising the variation found at position 1726 of SEQ ID NO: 83 where the nucleotides AACGTG in are present in a resistant pig and a 6 basepair deletion is observed in an ETEC susceptible pig.

A NA probe may be specific for an allele of at least one genetic polymorphism comprising the variation found at position 2009 of SEQ ID NO: 83, where pigs either dislay a T or a deletion of the T; the variation found at position 332 of SEQ ID NO: 87, where a SNP shifting between G and A is present; and the variation found at position 3530 of SEQ ID NO: 88, where a SNP shifting between G and A is present. Without being bound by theory, these three genetic polymorphisms are believed to be associated to resistance ETEC.

In an preferred embodiment of the present invention, the NA probe is capable of hybridising to a part of the allele which comprises the genetic polymorphism or to a NA sequence which is complementary to the part of the allele which comprises the genetic polymorphism.

The NA probe may be specific for an allele of a genetic polymorphism linked to resistance to ETEC, said allele of a genetic polymorphism linked to resistance to ETEC being linked to resistance to ETEC at a lod score of at least 3.0 including at least 4.0, 5.0, 6.0, 7.0, 8.0 or 9.0, 10 such as at least 50.

The NA probe may also in an interesting embodiment comprise a NA sequence that is homologous to the NA sequence of SEQ ID NO: 66 or its complementary sequence.

In useful embodiments, the NA probe comprises at least 10 nucleotides, such as at least 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250, 300, 400, such as at least 500 nucleotides. A presently preferred NA probe comprises from 10 to 30 nucleotides, such as from 15 to 23 nucleotides. In further useful embodiments, the NA probe comprises 15 nucleotides such as 16, 17, 18, 19, 20, 21, 22 or 23 nucleotides.

In a further aspect of the present invention there is provided a method for identifying if a pig is resistance to ETEC, the method comprising

-   -   i) obtaining a sample from said pig, said sample comprising         genetic material;     -   ii) determining by use of said sample if the pig is homozygous         for an allele of a genetic polymorphism linked to resistance to         ETEC, said genetic polymorphism being located In the region         between and including the markers SW2196 and SW225 on the         porcine chromosome 13; and     -   iii) identifying the pig as resistant to ETEC if the pig is         homozygous for the allele of genetic polymorphism linked to         resistance.

In one embodiment of the invention, the method further comprises identifying if the pig is non-resistance to ETEC and a carrier or a non-carrier of resistance, said method further comprises

-   -   iv) determining by use of said sample if the pig is heterozygous         or non-carrier of the allele of the genetic polymorphism linked         to resistance to ETEC; and     -   v) identifying         -   a) the pig as non-resistant to ETEC and a non-carrier of             resistance, if the pig is a non-carrier of the allele of the             genetic polymorphism linked to resistance; or that         -   b) the pig as non-resistant to ETEC but a carrier of             resistance if the pig is heterozygous for the allele of the             genetic polymorphism linked to resistance to ETEC.

In another embodiment of the invention, the genetic polymorphism is not located within the porcine chromosome 6. In a further embodiment, the genetic polymorphism is not located in the porcine alpha-(1,2) fucosyl-transferase gene (FUT1 gene).

In a preferred embodiment, the genetic polymorphism is located in the region flanked by and Including the markers SW2196 and SW225, such as the region flanked by and including the markers SW207 and S0075.

The most commonly used genetic markers for linkage mapping in pigs are microsatellites (e.g. SW2196, SW225, SW207 and S0075 and the other markers of Table 1 below), where the core of the marker is a tandemly-repeated sequence of two (usually) or a small number of nucleotides, where different alleles are distinguished by having different numbers of repeats. For microsatellites (and for many of the other possible marker types), the polymerase chain reaction (PCR) is used to amplify a small DNA sample and provides the first step in Identifying alternative alleles (i.e. genotyping). Unique PCR primers are used to ensure that only alleles of the specific marker of interest are amplified from the DNA sample of an individual animal. The PCR products are then separated by electrophoresis and can be visualised, for example via use of radioactive or fluorescent labels. The use of PCR on DNA-based markers means that genotyping can be performed on very small samples of DNA, which can be relatively easily collected at any time. Hence animals can be genotyped as soon as they are born using DNA isolated from blood, ear notches or other material.

The genetic polymorphism may be any genetic polymorphism located in the region between and including the markers SW2196 and SW225 on the porcine chromosome 13, wherein the allele of the genetic polymorphism linked to resistance to ETEC is linked to resistance to ETEC at a lod score of at least 3.0, including at least 4.0, 5.0, 6.0, 7.0, 8.0, 9.0 or 10.0, such as at least 50.

In another embodiment, the genetic polymorphism is located in the porcine MUC4 gene and/or in the adjacent genomic sequences at 3′ and/or 5′ end of the MUC4 gene. The adjacent genomic sequences may be the at less than 500 kb (kilobases) such as less than 300 kb or even less than 100 kb.

In a presently preferred embodiment of the invention the genetic polymorphism is located in a genomic sequence corresponding to SEQ ID NO: 6 and/or SEQ ID NO: 8. These sequences are believed to be a part of the porcine MUC4 gene. However, the genetic polymorphism may also be located in a genomic sequence corresponding to a nucleotide sequence selected from the group of SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 7, SEQ ID NO: 9, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 13, SEQ ID NO: 14, SEQ ID NO: 15, SEQ ID NO: 16, SEQ ID NO: 17, SEQ ID NO: 81, SEQ ID NO: 82, SEQ ID NO: 83, SEQ ID NO: 84, SEQ ID NO: 85, SEQ ID NO: 86, SEQ ID NO: 87, SEQ ID NO: 88, SEQ ID NO: 89, SEQ ID NO: 90, SEQ ID NO: 91, SEQ ID NO: 92, SEQ ID NO: 93, SEQ ID NO: 94, SEQ ID NO: 95, SEQ ID NO: 96, SEQ ID NO: 97, SEQ ID NO: 98, SEQ ID NO: 99, SEQ ID NO: 100, SEQ ID NO: 101, SEQ ID NO: 102, SEQ ID NO: 103, SEQ ID NO: 104, SEQ ID NO: 105, SEQ ID NO: 106, SEQ ID NO: 107, SEQ ID NO: 108, SEQ ID NO: 109, SEQ ID NO: 110, SEQ ID NO: 111, SEQ ID NO: 112, SEQ ID NO: 113, SEQ ID NO: 114, SEQ ID NO: 115, SEQ ID NO: 116, SEQ ID NO: 117, SEQ ID NO: 118, SEQ ID NO: 119, SEQ ID NO: 120, SEQ ID NO: 121, SEQ ID NO: 122, SEQ ID NO: 123, SEQ ID NO: 124, SEQ ID NO: 125, SEQ ID NO: 126, SEQ ID NO: 127, SEQ ID NO: 128, SEQ ID NO: 129, SEQ ID NO: 130, SEQ ID NO: 131, SEQ ID NO: 132, SEQ ID NO: 133, SEQ ID NO: 134, SEQ ID NO: 135, SEQ ID NO: 136, SEQ ID NO: 137, SEQ ID NO: 138, SEQ ID NO: 139, SEQ ID NO: 140, SEQ ID NO: 141, SEQ ID NO: 142, SEQ ID NO: 143, SEQ ID NO: 144, SEQ ID NO: 145, SEQ ID NO: 146, SEQ ID NO: 147, SEQ ID NO: 148, SEQ ID NO: 149, SEQ ID NO: 150, SEQ ID NO: 151, SEQ ID NO: 152, SEQ ID NO: 153, SEQ ID NO: 154, SEQ ID NO: 155, SEQ ID NO: 156, SEQ ID NO: 157, SEQ ID NO: 158, SEQ ID NO: 159, SEQ ID NO: 160, SEQ ID NO: 161, SEQ ID NO: 162, SEQ ID NO: 163, SEQ ID NO: 164, SEQ ID NO: 165, SEQ ID NO: 166, SEQ ID NO: 167, SEQ ID NO: 168, SEQ ID NO: 169, SEQ ID NO: 170, SEQ ID NO: 171, SEQ ID NO: 172, SEQ ID NO: 173, SEQ ID NO: 174, SEQ ID NO: 175, SEQ ID NO: 176, SEQ ID NO: 177, SEQ ID NO: 178, SEQ ID NO: 179, SEQ ID NO: 180, SEQ ID NO: 181, SEQ ID NO: 182, SEQ ID NO: 183, SEQ ID NO: 184, SEQ ID NO: 185, SEQ ID NO: 186, SEQ ID NO: 187, SEQ ID NO: 188, SEQ ID NO: 189, SEQ ID NO: 190, SEQ ID NO: 191, SEQ ID NO: 192, SEQ ID NO: 193, SEQ ID NO: 194, SEQ ID NO: 195, SEQ ID NO: 196, SEQ ID NO: 197, any fragments thereof and any 15 combinations thereof.

In an embodiment of the present invention, the genetic polymorphism is located in the porcine MUC4 gene.

Also, the genetic polymorphism comprises genetic polymorphisms that is in complete or nearly complete linkage disequilibrium with genetic polymorphisms mentioned above. The genetic polymorphisms according to the present invention may be identified as described in the Examples, e.g. in Example 6.

The terms “resistant to ETEC” or “resistance to ETEC” relates in the present context to a pig being resistant to one or more levels of E. coli infection, e.g. resistant to intestinal adhesion by ETEC, resistant to intestinal colonisation by ETEC, resistant to intestinal disorders, such as diarrhoea, caused by ETEC and any combination thereof. A pig resistant to a certain ETEC strain will be less susceptible to intestinal adhesion by ETEC and/or intestinal colonisation by ETEC and/or intestinal disorders caused by ETEC than a pig, which is non-resistant, when the two pigs are exposed to a similar dose of ETEC. In an useful embodiment of the present invention, the resistant pig is not susceptible to the ETEC at all.

In the case of intestinal adhesion, resistance vs. non-resistance is determined using the Adhesion test as described in Sellwood et al., 1975.

Briefly described, the Adhesion test may be performed in the following fashion: Epithelial cells from the upper part of the small intestine are obtained from specimens collected after slaughter of the pig. The adhesion test is performed by incubating the epithelial cells with e.g. E. coli F4ab and E. coli F4ac, respectively. Samples containing e.g. 10 to 20 epithelial cells may be examined for adhesion of both E. coli F4ab and E. coli F4ac by interference contrast microscopy. The results may be scored from 1 to 4, where 1=no bacteria adhering to the intestinal cells and 4=bacteria adhering to the whole brush border of all cells. If the score is 1, then the animal is considered to be resistant to intestinal adhesion by the respective ETEC (in this case to E. coli F4ab and E. coli F4ac). Alternatively, the pig may be considered to be resistant to intestinal adhesion by ETEC if the score is either 1 or 2.

In the case of intestinal colonisation by ETEC, resistance vs. non-resistance may be determined e.g. using an ETEC cell count in a faeces sample from the pig or by determining the concentration of ETEC related fimbrie in the faeces sample. A resistant, infected pig will have a significantly lowered number of ETEC or concentration of ETEC related fimbrie in the faeces sample than a non-resistant, infected pig.

In the case of intestinal disease by ETEC, resistance vs. non-resistance may be determined e.g. by feeding the pig a dose of ETEC and observe whether it develops an intestinal disease caused by the ETEC. If the pig develops the disease it is non-resistant. If the pig does not develop the disease it may either mean that the pig is resistant or that the pig is non-resistant, but for some reason it has not developed the intestinal disease. Administering drugs or special diets that compensate for non-resistance to the pig, might result in that a non-resistant pig does not develop the intestinal disease upon ETEC exposure.

The pig may either be male or female, and may have any age at the time of either determination and/or use of the identification of resistance or non-resistance. Thus, the pig may be selected from the group consisting of a boar, a sow, a suckling piglet, a weaned pig, a grower pig and a finisher pig. At the time of either determination and/or use of the identification of resistance or non-resistance, the pig may be unborn or have an age of 1 day to 1 month, 1-2 months, 2-3 months, 3-4 months, 4-5 months, 5-6 months, 6-7 months, 7-8 months, 8-9 months, 9-10 months, 10-11 months, 11-12 months, 12-14 months, 14-16 months, 16-18 months, 18-20 months, 20-24 months, 2-3 years, 3-4 years, 3-4 years, 4-5 years, 5-6 years, 6-7 years, 7-8 years or 8-10 years.

In an embodiment of the invention, the pig has a known pedigree, e.g. with known ancestors at least 1 generation back, such as at least 2 generations back, including at least 3, 4, 5, 6, 7, 8, 9, 10, or 15, such as at least 20 generations back. The pig may be a highly inbred animal and may have a pedigree certificate.

In a presently preferred embodiment of the invention, the genetic polymorphism is a SNP or a combination of SNPs. The SNP may e.g. be a single nucleotide G/C polymorphism.

A presently preferred SNP may be selected from the group consisting of A1059G in SEQ ID NO: 6, T1125G in SEQ ID NO: 6, A1134G in SEQ ID NO: 6, C1138G in SEQ ID NO: 6, C1849G in SEQ ID NO: 8, C2129T in SEQ ID NO: 8, A4847G in SEQ ID NO: 82, T4913G in SEQ ID NO: 82, A4922G in SEQ ID NO: 82, C4926G in SEQ ID NO: 82, A1659T in SEQ ID NO: 83, T1666G in SEQ ID NO: 83, C1684A in SEQ ID NO: 83, T1740A in SEQ ID NO: 83, C1795T in SEQ ID NO: 83, T1820G in SEQ ID NO: 83, C1912T in SEQ ID NO: 83, G2997A in SEQ ID NO: 83 and G3277C in SEQ ID NO: 83.

When referring to a SNP, the used syntax is “XpositionY in SEQ ID NO: ZZ”, where position is the nucleotide number of the SNP in SEQ ID NO: ZZ and where X is the nucleotide of the non-resistant haplotype and Y is the nucleotide in the resistant haplotype. For example A1059G in SEQ ID NO: 6, means that there is a SNP in nucleotide number 1059 of the nucleotide sequence of SEQ ID NO:6, and further that nucleotide number 1059 is an adenosine monophosphate group if the pig is non-resistant and that nucleotide number 1059 is a guanosine monophosphate group if the pig is resistant.

When making a more general reference to a SNP the syntax “X/Y SNP” is used. This refers to SNP where the non-resistant pig has a X nucleotide at the SNP position and the resistant pig has a Y nucleotide at the SNP position. Thus, a G/C SNP means a guanosine monophosphate group if the pig is resistant and a cytosine monophosphate group if the pig is non-resistant.

According to the present invention the SNP may be any single nucleotide polymorphism, such as a G/C single nucleotide polymorphism, a G/A single nucleotide polymorphism, a T/C single nucleotide polymorphism, a G/T single nucleotide polymorphism, an A/T single nucleotide polymorphism or a C/A single nucleotide polymorphism.

In an embodiment of the present invention, the method further comprising

-   -   in step ii), determining in the sample if the pig in addition to         the allele of the first genetic polymorphism linked to         resistance to ETEC, is homozygous, heterozygous or non-carrier         for an allele of an at least second genetic polymorphism linked         to resistance to ETEC, and     -   in step iii) identifying the pig as resistant to ETEC if the pig         is homozygous for the first allele of the genetic polymorphism         linked to resistance to ETEC and/or for the at least second         allele of the genetic polymorphism linked to resistance to ETEC.

The at least second genetic polymorphism may comprise at least 3 genetic polymorphisms, such as at least 4, 5, 6, 7, 10, 20, 30 or at least 50 genetic polymorphisms.

In preferred embodiments, the at least second genetic polymorphism is a genetic polymorphism selected from the group consisting of a single nucleotide polymorphism (SNP), a variable number tandem repeat polymorphism, an interspersed repetitive DNA, insertions, deletions, amplifications, rearrangements, a combination of SNP's, short tandem repeats, dinucleotide repeats, interspersed repetitive DNA and any combination of these.

The at least second polymorphism may be a SNP selected from the group consisting of A1059G in SEQ ID NO: 6, T1125G in SEQ ID NO: 6, A1134G in SEQ ID NO: 6, C1138G in SEQ ID NO: 6, C1849G in SEQ ID NO: 8, C2129T in SEQ ID NO: 8, A4847G in SEQ ID No: 82, T4913G in SEQ ID NO: 82, A4922G in SEQ ID NO: 82, C4926G in SEQ ID NO: 82, A1659T in SEQ ID NO: 83, T1666G in SEQ ID NO: 83, C1684A in SEQ ID NO: 83, T1740A in SEQ ID NO: 83, C1795T in SEQ ID NO: 83, T1820G in SEQ ID NO: 83, C1912T in SEQ ID NO: 83, G2997A in SEQ ID NO: 83 and G3277C in SEQ ID NO: 83.

In another embodiment of the invention, the at least second genetic polymorphism is located in the porcine FUT1 gene.

According to the method of the present invention, the sample obtained from the pig may be selected from the group consisting of a material comprising DNA and/or RNA, blood, saliva, tissue, throat swap, semen, and combinations thereof.

The method according to the invention includes providing a sample comprising genetic material. Such material comprises porcine DNA material, which may be provided by any conventional method or means. The porcine DNA material may e.g. be extracted, isolated and purified from blood (e.g., fresh or frozen), tissue samples (e.g., spleen, buccal smears), hair samples containing follicular cells and semen. The sample may comprise blood, partly or fully hydrolysed blood, saliva, tissue, throat swap, semen or combinations thereof.

The determination whether the pig is homozygous, heterozygous or non-carrier of the allele of the genetic polymorphism linked to resistance to ETEC may be performed using a technique selected from the group consisting of allele specific PCR, mini sequencing, primer extension, pyrosequencing, PCR-RFLP, allele-specific rolling circle amplification, ARMS (Amplification Refracting Mutation System), hybridisation e.g. to DNA arrays, DASH (Dynamic Allele-Specific Hybridisation), melting curve measurement, and primer extension followed by MALDI-TOF mass spectrometry and any combinations thereof.

The below Example 4 illustrates the use of PCR and DASH, respectively, for determining whether the pig is homozygous, heterozygous or non-carrier of the allele of the genetic polymorphism linked to resistance to ETEC.

A number of methods exist that can be used to detect single base mutations and other types of polymorphisms. Detailed description of useful methods may be found in Ausubel et al. (2000) and in Sambrook et al. (1989). Among the more important methods are: DNA sequencing; single strand conformation polymorphism (SSCP) method; denaturing gradient gel electrophoresis (DGGE) method; dideoxy fingerprinting, restriction endonuclease fingerprinting and constant denaturing gel electrophoresis (CDGE). Mutations can also be detected by specific hybridisation of oligonucleotides to the nucleic acid to be analysed.

The determination of whether the pig is homozygous, heterozygous or non-carrier of the allele of the genetic polymorphism linked to resistance to ETEC may be performed using a method which comprises at least one of the following steps

-   -   a) obtaining a sample from the pig, said sample comprising         genetic material;     -   b) extracting genomic DNA from said sample;     -   c) amplifying at least a fragment of the genomic DNA to obtain         an amplification product;     -   d) contacting the amplification product with a restriction         enzyme;     -   e) separating the resulting fragments by gel electrophoresis;     -   f) determining the respective numbers and lengths of fragments;         and     -   g) determining from the number and lengths which polymorphism is         present.

The method of determination may be performed in the sequence a), b), c), d), e), f) and g).

The restriction enzyme may be an enzyme such as Aat II, Bam HI, BgI II, Cla I (Bsu 151), Dpn I, Eco RI, Eco RV, Esp I (Bpu 1102I), Hind III, Nco I, Nde I, Not I, Pae I (Sph I), Pau I, Pst I, Pvu I, Sac I, Sal I, Sma I, Xba I or Xho I.

The restriction enzyme XbaI is preferred when the allele of the genetic polymorphism linked to resistance to ETEC is the SNP C1849G.

In preferred embodiments, the ETEC is selected from the group consisting of E. coli F4ab/F4ac, E. coli 0149, E. coli F4, E. coli F18, E. coli F5, E. coli F6, E. coli 987P, E. coli F41, E. coli F18ab, E. coli F107, E. coli F18ac, E. coli 2134P and E. coli Av24, and any combinations of these organisms.

The present invention further relates to the use of the isolated NA molecule as described herein and/or the NA probe as described herein, as a probe for detecting an allele of a genetic polymorphism linked to resistant to ETEC.

A further aspect of the present invention relates to the use of a pair of NA molecules for primers in a PCR-based method, said PCR-based method being used in a method for identifying whether a pig is resistant or non-resistant to ETEC, said pair of NA molecules being selected from the group consisting of SEQ ID NO: 18 and SEQ ID NO: 19, SEQ ID NO: 20 and SEQ ID NO: 21, SEQ ID NO: 22 and SEQ ID NO: 23, SEQ ID NO: 24 and SEQ ID NO: 25, SEQ ID NO: 26 and SEQ ID NO: 27, SEQ ID NO: 28 and SEQ ID NO: 29, SEQ ID NO: 30 and SEQ ID NO: 31, SEQ ID NO: 32 and SEQ ID NO: 33, SEQ ID NO: 34 and SEQ ID NO: 35, SEQ ID NO: 36 and SEQ ID NO: 37, SEQ ID NO: 38 and SEQ ID NO: 39, SEQ ID NO: 40 and SEQ ID NO: 41, SEQ ID NO: 42 and SEQ ID NO: 43, SEQ ID NO: 44 and SEQ ID NO: 45, SEQ ID NO: 46 and SEQ ID NO: 47, SEQ ID NO: 48 and SEQ ID NO: 49, SEQ ID NO: 50 and SEQ ID NO: 51, SEQ ID NO: 52 and SEQ ID NO: 53, SEQ ID NO: 54 and SEQ ID NO: 55, SEQ ID NO: 56 and SEQ ID NO: 57, SEQ ID NO: 58 and SEQ ID NO: 59, SEQ ID NO: 60 and SEQ ID NO: 61, SEQ ID NO: 62 and SEQ ID NO: 63, SEQ ID NO: 64 and SEQ ID NO: 65 and their complementary sequences.

The present invention is not restricted to using the pairs mentioned herein, thus the NA sequences in SEQ ID NO: 18, SEQ ID NO: 19, SEQ ID NO: 20, SEQ ID NO: 21, SEQ ID NO: 22, SEQ ID NO: 23, SEQ ID NO: 24, SEQ ID NO: 25, SEQ ID NO: 26, SEQ ID NO: 27, SEQ ID NO: 28, SEQ ID NO: 29, SEQ ID NO: 30, SEQ ID NO: 31, SEQ ID NO: 32, SEQ ID NO: 33, SEQ ID NO: 34, SEQ ID NO: 35, SEQ ID NO: 36, SEQ ID NO: 37, SEQ ID NO: 38, SEQ ID NO: 39, SEQ ID NO: 40, SEQ ID NO: 41, SEQ ID NO: 42, SEQ ID NO: 43, SEQ ID NO: 44, SEQ ID NO: 45, SEQ ID NO: 46, SEQ ID NO: 47, SEQ ID NO: 48, SEQ ID NO: 49, SEQ ID NO: 50, SEQ ID NO: 51, SEQ ID NO: 52, SEQ ID NO: 53, SEQ ID NO: 54, SEQ ID NO: 55, SEQ ID NO: 56, SEQ ID NO: 57, SEQ ID NO: 58, SEQ ID NO: 59, SEQ ID NO: 60, SEQ ID NO: 61, SEQ ID NO: 62, SEQ ID NO: 63, SEQ ID NO: 64 and SEQ ID NO: 65 may all be used for primers in a PCR-based process, said PCR-based process being a step in a method for identifying whether a pig is resistant or non-resistant to ETEC.

Also, the pair of NA molecules for primers in a PCR-based method may comprise a NA molecules being selected from the group consisting of SEQ ID NO: 18 and SEQ ID NO: 19, SEQ ID NO: 20 and SEQ ID NO: 21, SEQ ID NO: 22 and SEQ ID NO: 23, SEQ ID NO: 24 and SEQ ID NO: 25, SEQ ID NO: 26 and SEQ ID NO: 27, SEQ ID NO: 28 and SEQ ID NO: 29, SEQ ID NO: 30 and SEQ ID NO: 31, SEQ ID NO: 32 and SEQ ID NO: 33, SEQ ID NO: 34 and SEQ ID NO: 35, SEQ ID NO: 36 and SEQ ID NO: 37, SEQ ID NO: 38 and SEQ ID NO: 39, SEQ ID NO: 40 and SEQ ID NO: 41, SEQ ID NO: 42 and SEQ ID NO: 43, SEQ ID NO: 44 and SEQ ID NO: 45, SEQ ID NO: 46 and SEQ ID NO: 47, SEQ ID NO: 48 and SEQ ID NO: 49, SEQ ID NO: 50 and SEQ ID NO: 51, SEQ ID NO: 52 and SEQ ID NO: 53, SEQ ID NO: 54 and SEQ ID NO: 55, SEQ ID NO: 56 and SEQ ID NO: 57, SEQ ID NO: 58 and SEQ ID NO: 59, SEQ ID NO: 60 and SEQ ID NO: 61, SEQ ID NO: 62 and SEQ ID NO: 63, SEQ ID NO: 64 and SEQ ID NO: 65 and their complementary sequences.

It will be understood, that the present invention is not restricted to using the pairs mentioned herein, thus the NA sequences in SEQ ID NO: 18, SEQ ID NO: 19, SEQ ID NO: 20, SEQ ID NO: 21, SEQ ID NO: 22, SEQ ID NO: 23, SEQ ID NO: 24, SEQ ID NO: 25, SEQ ID NO: 26, SEQ ID NO: 27, SEQ ID NO: 28, SEQ ID NO: 29, SEQ ID NO: 30, SEQ ID NO: 31, SEQ ID NO: 32, SEQ ID NO: 33, SEQ ID NO: 34, SEQ ID NO: 35, SEQ ID NO: 36, SEQ ID NO: 37, SEQ ID NO: 38, SEQ ID NO: 39, SEQ ID NO: 40, SEQ ID NO: 41, SEQ ID NO: 42, SEQ ID NO: 43, SEQ ID NO: 44, SEQ ID NO: 45, SEQ ID NO: 46, SEQ ID NO: 47, SEQ ID NO: 48, SEQ ID NO: 49, SEQ ID NO: 50, SEQ ID NO: 51, SEQ ID NO: 52, SEQ ID NO: 53, SEQ ID NO: 54, SEQ ID NO: 55, SEQ ID NO: 56, SEQ ID NO: 57, SEQ ID NO: 58, SEQ ID NO: 59, SEQ ID NO: 60, SEQ ID NO: 61, SEQ ID NO: 62, SEQ ID NO: 63, SEQ ID NO: 64 and SEQ ID NO: 65 may all be used for primers in a PCR-based process, said PCR-based process being a step in a method for identifying whether a pig is resistant or non-resistant to ETEC.

At least one primer of the pairs of primers may comprise a NA sequence or a fragment of a NA sequence, said NA sequence being selected from the group consisting of SEQ ID NO: 18, SEQ ID NO: 19, SEQ ID NO: 20, SEQ ID NO: 21, SEQ ID NO: 22, SEQ ID NO: 23, SEQ ID NO: 24, SEQ ID NO: 25, SEQ ID NO: 26, SEQ ID NO: 27, SEQ ID NO: 28, SEQ ID NO: 29, SEQ ID NO: 30, SEQ ID NO: 31, SEQ ID NO: 32, SEQ ID NO: 33, SEQ ID NO: 34, SEQ ID NO: 35, SEQ ID NO: 36, SEQ ID NO: 37, SEQ ID NO: 38, SEQ ID NO: 39, SEQ ID NO: 40, SEQ ID NO: 41, SEQ ID NO: 42, SEQ ID NO: 43, SEQ ID NO: 44, SEQ ID NO: 45, SEQ ID NO: 46, SEQ ID NO: 47, SEQ ID NO: 48, SEQ ID NO: 49, SEQ ID NO: 50, SEQ ID NO: 51, SEQ ID NO: 52, SEQ ID NO: 53, SEQ ID NO: 54, SEQ ID NO: 55, SEQ ID NO: 56, SEQ ID NO: 57, SEQ ID NO: 58, SEQ ID NO: 59, SEQ ID NO: 60, SEQ ID NO: 61, SEQ ID NO: 62, SEQ ID NO: 63, SEQ ID NO: 64 and SEQ ID NO: 65.

A useful primer may comprise a fragment of a NA sequence selected from the group consisting of SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 7, SEQ ID NO: 9, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 13, SEQ ID NO: 14, SEQ ID NO: 15, SEQ ID NO: 16, SEQ ID NO: 17, SEQ ID NO: 81, SEQ ID NO: 82, SEQ ID NO: 83, SEQ ID NO: 84, SEQ ID NO: 85, SEQ ID NO: 86, SEQ ID NO: 87, SEQ ID NO: 88, SEQ ID NO: 89, SEQ ID NO: 90, SEQ ID NO: 91, SEQ ID NO: 92, SEQ ID NO: 93, SEQ ID NO: 94, SEQ ID NO: 95, SEQ ID NO: 96, SEQ ID NO: 97, SEQ ID NO: 98, SEQ ID NO: 99, SEQ ID NO: 100, SEQ ID NO: 101, SEQ ID NO: 102, SEQ ID NO: 103, SEQ ID NO: 104, SEQ ID NO: 105, SEQ ID NO: 106, SEQ ID NO: 107, SEQ ID NO: 108, SEQ ID NO: 109, SEQ ID NO: 110, SEQ ID NO: 111, SEQ ID NO: 112, SEQ ID NO: 113, SEQ ID NO: 114, SEQ ID NO: 115, SEQ ID NO: 116, SEQ ID NO: 117, SEQ ID NO: 118, SEQ ID NO: 119, SEQ ID NO: 120, SEQ ID NO: 121, SEQ ID NO: 122, SEQ ID NO: 123, SEQ ID NO: 124, SEQ ID NO: 125, SEQ ID NO: 126, SEQ ID NO: 127, SEQ ID NO: 128, SEQ ID NO: 129, SEQ ID NO: 130, SEQ ID NO: 131, SEQ ID NO: 132, SEQ ID NO: 133, SEQ ID NO: 134, SEQ ID NO: 135, SEQ ID NO: 136, SEQ ID NO: 137, SEQ ID NO: 138, SEQ ID NO: 139, SEQ ID NO: 140, SEQ ID NO: 141, SEQ ID NO: 142, SEQ ID NO: 143, SEQ ID NO: 144, SEQ ID NO: 145, SEQ ID NO: 146, SEQ ID NO: 147, SEQ ID NO: 148, SEQ ID NO: 149, SEQ ID NO: 150, SEQ ID NO: 151, SEQ ID NO: 152, SEQ ID NO: 153, SEQ ID NO: 154, SEQ ID NO: 155, SEQ ID NO: 156, SEQ ID NO: 157, SEQ ID NO: 158, SEQ ID NO: 159, SEQ ID NO: 160, SEQ ID NO: 161, SEQ ID NO: 162, SEQ ID NO: 163, SEQ ID NO: 164, SEQ ID NO: 165, SEQ ID NO: 166, SEQ ID NO: 167, SEQ ID NO: 168, SEQ ID NO: 169, SEQ ID NO: 170, SEQ ID NO: 171, SEQ ID NO: 172, SEQ ID NO: 173, SEQ ID NO: 174, SEQ ID NO: 175, SEQ ID NO: 176, SEQ ID NO: 177, SEQ ID NO: 178, SEQ ID NO: 179, SEQ ID NO: 180, SEQ ID NO: 181, SEQ ID NO: 182, SEQ ID NO: 183, SEQ ID NO: 184, SEQ ID NO: 185, SEQ ID NO: 186, SEQ ID NO: 187, SEQ ID NO: 188, SEQ ID NO: 189, SEQ ID NO: 190, SEQ ID NO: 191, SEQ ID NO: 192, SEQ ID NO: 193, SEQ ID NO: 194, SEQ-ID NO: 195, SEQ ID NO: 196, SEQ ID NO: 197, and their complementary sequences.

Preferred primers may comprise a fragment of a NA sequence selected from the group consisting of SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 7, SEQ ID NO: 9, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 13, SEQ ID NO: 14, SEQ ID NO: 15, SEQ ID NO: 16, SEQ ID NO: 17, SEQ ID NO: 81, SEQ ID NO: 82, SEQ ID NO: 83, SEQ ID NO: 84, SEQ ID NO: 85, SEQ ID NO: 86, SEQ ID NO: 87, SEQ ID NO: 88, SEQ ID NO: 89, SEQ ID NO: 90, SEQ ID NO: 91, SEQ ID NO: 92, SEQ ID NO: 93, SEQ ID NO: 94, SEQ ID NO: 95, SEQ ID NO: 96, SEQ ID NO: 97, SEQ ID NO: 98, SEQ ID NO: 99, SEQ ID NO: 100, SEQ ID NO: 101.

A useful pair of primers may comprise two primers as defined above. Preferably, one of these primers is complementary to the NA sequences of the mentioned SEQ ID NO:s.

In a preferred embodiment the primer pairs SEQ ID NO: 62 and SEQ ID NO: 63 or SEQ ID NO: 64 and SEQ ID NO: 65, are used as the amplify parts of the porcine MUC4 gene.

In accordance with the present invention there is also provided a kit for determining if a pig is homozygous, heterozygous or non-carrier of an allele of a genetic polymorphism linked to resistance to ETEC, said kit comprising a first component selected from the group consisting of a NA probe as described herein, a NA molecule as described herein, a pair of PCR-primers as described herein, a restriction enzyme and any combination thereof.

Useful primers may comprise a primer as described herein, such as a pair of PCR-primers may be selected from the group consisting of SEQ ID NO: 18 and SEQ ID NO: 19, SEQ ID NO: 20 and SEQ ID NO: 21, SEQ ID NO: 22 and SEQ ID NO: 23, SEQ ID NO: 24 and SEQ ID NO: 25, SEQ ID NO: 26 and SEQ ID NO: 27, SEQ ID NO: 28 and SEQ ID NO: 29, SEQ ID NO: 30 and SEQ ID NO: 31, SEQ ID NO: 32 and SEQ ID NO: 33, SEQ ID NO: 34 and SEQ ID NO: 35, SEQ ID NO: 36 and SEQ ID NO: 37, SEQ ID NO: 38 and SEQ ID NO: 39, SEQ ID NO: 40 and SEQ ID NO: 41, SEQ ID NO: 42 and SEQ ID NO: 43, SEQ ID NO: 44 and SEQ ID No: 45, SEQ ID NO: 46 and SEQ ID NO: 47, SEQ ID NO: 48 and SEQ ID NO: 49, SEQ ID NO: 50 and SEQ ID NO: 51, SEQ ID NO: 52 and SEQ ID NO: 53, SEQ ID NO: 54 and SEQ ID NO: 55, SEQ ID NO: 56 and SEQ ID NO: 57, SEQ ID NO: 58 and SEQ ID NO: 59, SEQ ID NO: 60 and SEQ ID NO: 61, SEQ ID NO: 62 and SEQ ID NO: 63, SEQ ID NO: 64 and SEQ ID NO: 65 and their complementary sequences.

The kit may further comprise at least a second component selected from the group consisting of a restriction enzyme, a pH-buffer, a gel, a washing buffer and an incubation buffer, or any combination thereof.

The kit may even further comprise an at least third component selected from the group consisting of a restriction enzyme, a pH-buffer, a gel, a washing buffer, an incubation buffer, and any combination thereof.

In a further aspect, the present invention relates to a method for breeding pigs that are resistant to ETEC, the method comprising

-   -   i) selecting a first pig, said pig identified as resistant to         ETEC using a method described herein; and     -   ii) breeding said first pig with a second pig,         to obtain a pig progeny that has a greater probability of being         resistant to ETEC than progeny from randomly chosen parent pigs.

Also, the method may be performed by breeding a first pig, which is identified as resistant to ETEC using a method described herein, with a second pig. The pig progeny obtained thereby will have a greater probability of being resistant to ETEC than progeny from randomly chosen parent pigs. The resistance/non-resistance of the second pig need not to be known.

However, In a preferred embodiment, the second pig is a pig chosen among pigs that are identified as resistant to ETEC using a method of identification as described herein.

In accordance with the present Invention, it may be useful to use a physical marking of a pig for identifying the pig as resistant or non-resistant to ETEC. The physical marking could comprise a sign to be read by the human eye, a barcode, a marking device capable of transmitting the information of resistance/non-resistance wireless to a receiving device.

In yet a further aspect, the present invention relates to an isolated NA molecules as described herein for the use as: an antisense-NA, an iRNA, a Rribosyme, an ETC for genetic medicine, gene therapy or cinetoplastic DNA repair.

In accordance with the present invention, there is also provided a method for producing pork meat, comprising the steps of i) obtaining a pig progeny with improved resistance as described herein, and ii) preparing pork meat from the pig progeny.

In accordance with the present invention, it may be useful to use a physical marking of a pig for identifying the pig as resistant or non-resistant to ETEC. The physical marking could comprise a sign to be read by the human eye, a barcode, a marking device capable of transmitting the information of resistance/non-resistance wireless to a receiving device.

In further aspect, the invention relates to the use of a genetic polymorphism to treat pigs that are non-resistant to ETEC, said genetic polymorphism being located in the region between and including the markers SW2196 and SW225 on the porcine chromosome 13. In a useful embodiment, the genetic polymorphism is located in the region flanked by and including the markers SW207 and S0075.

In a still further aspect, the present invention relates to a method for screening a potential drug candidate for treatment of non-resistance to ETEC, the method comprising the steps of

-   -   i) selecting a test population of pigs that are determined as         non-resistant to ETEC as described herein;     -   ii) administering the potential drug candidate to the test         population; and     -   iii) evaluation the efficacy of the potential drug candidate on         the test population.

In accordance with the present invention, the porcine MUC4 protein may be used as a drug to make a non-resistant pig resistance to ETEC.

Also encompassed by the present invention is a mixed boar semen, comprising semen from at least two boars, said boars being identified as resistant to ETEC using a method as defined herein. The number of boars contributing to the mix may be at least 3 such as at least 4, 5, 6, 7, 8, 10, 12, 15, 20, 25 such as at least 100 boars.

It will be understood, that the information of the presence or absence of the genetic polymorphism in a pig may conveniently be stored on a data storage medium. Such information of resistance/non-resistance in a data processing system may be used e.g. to control feeding, medication or breeding of the pigs.

Yet another aspect of the present invention provides a method for identifying if a pig is resistant or non-resistant to enterotoxigenic or enteropathogenic E. coli (ETEC), the method comprising:

i) obtaining a sample from said pig, said sample comprising genetic material;

ii) determining in said sample the presence or absence of a marker linked to resistance to ETEC, and

iii) inferring that the pig is resistant to ETEC, if the marker linked to resistance to ETEC is present in the sample.

In a useful embodiment of the invention, the marker comprises one or more of the components selected from the group consisting of a protein, a hormone and a genetic polymorphism. The marker may be considered present in the sample if the component is present in the sample. Also, the marker may be considered present in the sample if the concentration of the component in the sample is e.g. above a certain threshold, below a certain threshold, within a certain concentration interval or outside a certain concentration interval.

When the marker comprises a protein, this protein may be porcine MUC4, or a porcine mucin-like protein. The protein may also well be a transferrin receptor protein or a protein with a transferrin-receptor-like activity.

Also encompassed by the present invention is a probe specific for the marker linked to resistance to ETEC.

The probe may comprise a binding element selected from the group consisting of a polyclonal antibody, a monoclonal antibody, a receptor, a ligand. In a preferred embodiment the probe is an antibody or a ligand specific for the MUC4 protein.

The invention is further illustrated in the following non-limiting examples and in the figures, wherein

FIG. 1. illustrates the linkage map showing the location of the F4ab/F4ac locus (in bold)

FIG. 2. shows a comparative mapping of the porcine chromosome 13 (SSC13) and the human chromosome 3 (HSA3) with the BAC sequences;

FIG. 3. shows a comparative map between SSC13 and HSA3 using the mapping results in this application;

FIG. 4. illustrates contig of the MUC4 pigEBACs;

FIG. 5. illustrates the sequencing status along with the SNP information using the human Mucin 4 genme as scaffold. The aligned porcine sequences are indicated by the solid lines over exons, vertical bars indicate exons;

FIG. 6. shows the sequence surrounding the XbaI polymorphism (SEQ ID NO:. 67). The SNP of the resistant allele is shown in bold and underlined; and

FIG. 7. shows the sequence surrounding the XbaI polymorphism (SEQ ID NO:. 68). The SNP of the sensitive allele is shown in bold and underline.

EXAMPLES Example 1 Identification of the Gene Responsible for Resistance Towards E. coli ETEC F4ab/F4ac Diarrhoea 1.1. Introduction

In order to characterise the gene responsible for resistance towards E. coli F4ab/F4ac diarrhoea it was decided to rely on the so-called ‘positional candidate gene cloning’ strategy (Collins 1995). The starting point was the work described by Edfors-Lilja and co-workers in 1995. This study was significantly expanded by increasing the DNA-marker density on the pig chromosome 13 (SSC13) linkage map in the same intercross pedigree that was used in the Edfors-Lilja analysis. In addition the gene mapping in the chromosomal area where the gene responsible for resistance towards ETEC F4ab/F4ac is localised were significantly improved.

In the following the work is described that was carried out in order to identify candidate genes and resulted in the identification of polymorphisms in a candidate gene showing strong linkage disequilibrium with ETEC F4ab/F4ac status in pigs.

1.2 Linkage Analysis

Animals

In the linkage analysis we used the pedigree described by Edfors-Lilja et al. (1995). The parental generation comprised two European Wild boars each mated to four Swedish Yorkshire sows. The Fl generation was intercrossed (four sires and 22 dams) to generate 200 F2 offspring. In order to obtain large full-sib families, the maitings were repeated, and the offspring were consequently born in two parities.

Adhesion Test

Epithelial cells from the upper part of the small intestine were obtained from specimens collected after slaughter of all animals. The adhesion test was performed by incubating the epithelial cells with E. coli F4ab and E. coli F4ac, respectively. Samples containing 10 to 20 cells were examined for adhesion of both E. coli F4ab and E. coli F4ac by interference contrast microscopy. The results were scored from 1 to 4, where 1=no bacteria and 4=bacteria adhering to the whole brush border of all cells (Edfors-Lilja et al., 1996).

Genotyping

Microsatellite markers (i.e. markers where the core of the marker is a tandemly-repeated sequence of two (usually) or a small number of nucleotides, where different alleles are distinguished by having different numbers of repeats) were used as genetic markers for linkage mapping.

In the present work 60 microsatellites markers from the porcine chromosome 13 (SSC13) were selected from the USDA linkage map (Rohrer et al. 1996)

One PCR primer from each of the 60 markers were fluorescently labelled with either 6-FAM, HEX or TET (Applied Biosystems, Foster City, Calif., USA) and Polymerase Chain Reaction (PCR) was carried out in a PE9600 thermocycler (Applied Blosystems, Foster City, Calif., USA) or an ABI877 (Applied Blosystems, Foster City, Cailf., USA) using 10 μl reaction volume containing 25 ng genomic DNA, 1×PCR buffer, 1.5-2.0 mM MgCl₂, 200 μM of each dNTP, 0.35 μM of each primer, and 0.25 units AmpliTaq Gold DNA polymerase (Applied Biosystems, Foster City, Calif., USA). Thermocycling conditions were: pre-denaturation for 10 min at 95° C., followed by 10 cycles with decreasing annealing temperatures (15 sec at 95° C., 30 sec at 64°-55° C., 60 sec at 72° C.), 25 cycles of reaction with a fixed annealing temperature (15 sec at 89° C., 30 sec at 55° C., 60 sec at 72° C.), and extension at 72° C. for 1 hour.

PCR products were loaded on 4.25% polyacrylamide denaturing sequencing gel, and run on an ABI PRISM 377 DNA sequencer. The PCR products were analyzed using the GeneScan 2 software (Applied Biosystems, Foster City, Calif., USA). Markers that amplified well, that were easy to score and showed heterozygosity in the F1-generation of the pedigree were selected for the linkage mapping in all 236 animals. In alphabetical order the following markers were used:

CP, EST24F05, PR39, S0075, S0076, S0215, 50219, S0222, S0281, S0282, S0291, SW1030, SW1056, SW1864, SW1898, SW207, SW2196, SW225, SW2412, SW398, SW458, SW698, SW769, SW864, SW873, SW882, SW937, SW955, SWRlOO8, SWR428, SWR926, and TF.

Detailed descriptions of the genetic markers can be found on the Web site of the USDA Meat Animal Research Center and in the pig genome database (ArkDB database) available on a website hosted at Roslin Institute.

Alleles were assigned and genotyping data was managed using the GEMMA software (Iannuccelli, 1996). The genotyping data were used for the construction of a SSC13 linkage map. The linkage analysis was performed using CRIMAP version 2.4 (Green et al. 1990). Initially, the option TWOPOINT was used to find linkage between the markers with a lod score higher than three. Subsequently, the option BUILD was used to construct the framework map and the remaining markers were incorporated using the option ALL. Finally, the genotypes were checked using the option CHROMPIC and the data was scrutinized for any unlikely double-recombinants.

The results of the linkage analysis map is shown in Table 1.

When the data for the F4ab/F4ac locus (the location of the gene conferring resistance/susceptibility to ETEC F4 induced disease) are added the most likely position for this locus is proximal to S0075 and it is supported by a lod score of 1.91 in comparison to the next best order where ETEC F4ab/F4ac locus is located distal to S0075. So the conclusion from the linkage analysis is the following position of F4ab/F4ac is CEN-SW207-F4ab/F4ac-S0075-TEL. The linkage map showing the position of the F4ab/F4ac locus is shown in FIG. 1

TABLE 1 The generated linkage map (sex averaged) Marker Recombination cM Kosambi cM S0282 0.0 S0219 0.07 6.7 6.7 SWR428 0.20 21.8 28.5 S0076 0.14 14.3 42.9 PR39 0.15 15.6 58.4 SW458 0.04 4.4 62.9 SW864 0.04 3.8 66.7 EST24F05 0.00 0.0 66.7 S0222 0.09 9.2 75.9 SWR1008 0.01 0.9 76.8 SW1864 0.03 3.3 80.1 SW2412 0.02 2.1 82.1 SW937 0.02 1.6 83.7 SW882 0.02 1.5 85.2 SWR926 0.00 0.0 85.2 S0281 0.01 0.6 85.8 TF 0.03 2.5 88.4 CP 0.01 1.1 89.4 SW1898 0.03 2.9 92.4 SW2196 0.01 1.0 93.4 SW207 0.01 1.2 94.6 S0075 0.05 4.9 99.4 SW225 0.02 2.2 101.6 SW955 0.01 0.8 102.5 SW873 0.02 1.8 104.3 SW1030 0.01 0.5 104.8 SW698 0.02 2.0 106.8 SW398 0.04 3.8 110.6 SW1056 0.16 16.7 127.3 SW769 0.16 17.1 144.4 S0215 0.03 3.4 147.8 S0291 0.12 12.3 160.1

1.3 Cytogenetic Mapping

To obtain a physical map of the region containing the gene responsible for resistance owards E. coli F4ab/F4ac diarrhoea microsatellites markers surrounding the F4ab/F4ac locus were used to screen a pig BAC library (Anderson et al. 2000). The pig BAC library is a collection of large fragments of pig genomic DNA (average size=150,000 base pairs) in which each fragment is maintained in a bacterial artificial chromosome (BAC) cloning vector immortalised in a clone of E. coli bacteria.

In the present study the Roslin pigE BAC library, which consists of approximately 100,000 independent BAC clones stored as individual clones in 96-well and 384-well microplates was used. This library provides an approximately five fold coverage of the pig genome. The BAC clones were identified using PCR primers from markers Sw207, S0283, S0075, Sw1876 and Sw225 on DNA pools from the BAC clones.

DNA was extracted from the marker-positive BAC clones using the Qiagen Plasmid Midiprep kit (Qiagen, Germany) and the BACs were individually labelled with biotin-14-dATP or digoxigenin-11-dUTP (Boehringer-Mannheim, Germany) both single-colour and dual-colour fluorescent in situ hybridisation (FISH) analysis to porcine metaphase and interphase chromosomes (as described in Chowdhary et al., 1995).

The physical order of the markers were shown to be in accordance with the linkage data namely CEN-Sw207-50283-S0075-Sw1876-Sw225-TEL. BACs containing markers Sw207, S0283 and S0075 were all hybridising to pig chromosome 13 band q41 indicating that this is the candidate region. Primers for amplifying the markers mentioned herein are listed in Table 2.

TABLE 2 Sequences related to the invention SEQ ID NO: Description of sequence 1 Genomic pig DNA showing similarity to the human Mucin 4 gene exon 2 (GenBank acc. No. AJ430032). 2 Genomic pig DNA showing similarity to the human Mucin 4 gene intron 3, exon 4 (GenBank acc. No. AJ430033). 3 Genomic pig DNA showing similarity to the human Mucin 4 gene exon 4 (GenBank acc. No. AJ430033). 4 Genomic pig DNA showing similarity to the human Mucin 4 gene intron 4, exon 5 (GenBank acc. No. AJ430034). 5 Genomic pig DNA showing similarity to the human Mucin 4 gene exon 5, intron 5 (GenBank acc. No. AJ430034). 6 Genomic pig DNA showing similarity to the human Mucin 4 gene exon 5, intron 5 (GenBank acc. No. AJ430034). Variation found at position 1059: G in resistant, A in susceptible Variation found at position 1125: G in resistant, T in susceptible Variation found at position 1134: G in resistant, A in susceptible Variation found at position 1138: G in resistant, C in susceptible 7 Genomic pig DNA showing similarity to the human Mucin 4 gene intron 6 (GenBank acc. No. AJ430034). 8 Genomic pig DNA showing similarity to the human Mucin 4 gene intron 7, exon 8, intron 8 (GenBank acc. No. AJ430034). Variation found at position 1849: G in resistant, C in susceptible Variation found at position 2129: T in resistant, C in susceptible 9 Genomic pig DNA showing similarity to the human Mucin 4 gene exon 17 (GenBank acc. No. AJ430034). 10 Genomic pig DNA showing similarity to the human Mucin 4 gene intron 17 (GenBank acc. No. AJ430034). 11 Genomic pig DNA showing similarity to the human Mucin 4 gene intron 18 (GenBank acc. No. AJ430034). 12 Genomic pig DNA showing similarity to the human Mucin 4 gene exon 20 (GenBank acc. No. AJ430034). 13 Genomic pig DNA showing similarity to the human Mucin 4 gene exon 22 (GenBank acc. No. AJ430034). 14 Genomic pig DNA showing similarity to the human Mucin 4 gene exon 23 (GenBank acc. No. AJ430034). 15 Genomic pig DNA showing similarity to the human Mucin 4 gene intron 23 (GenBank acc. No. AJ430034). 16 Genomic pig DNA showing similarity to the human Mucin 4 gene exon 24 (GenBank acc. No. AJ430034). 17 Porcine cDNA sequence showing similarity to Homo sapiens MUC4 gene, 3′ flanking region (Genbank acc. no. AJ010901). 18 upper primer related to gene ADPRLT3 19 lower primer related to gene ADPRLT3 20 upper primer related to gene ARF4 21 lower primer related to gene ARF4 22 upper primer related to gene ARP 23 lower primer related to gene ARP 24 upper primer related to gene DKFZp434P0721 25 lower primer related to gene DKFZp434P0721 26 upper primer related to gene GPX1 27 lower primer related to gene GPX1 28 upper primer related to gene KIAA0804 29 lower primer related to gene KIAA0804 30 upper primer related to gene KIAA1363 31 lower primer related to gene KIAA1363 32 upper primer related to gene MME 33 lower primer related to gene MME 34 upper primer related to gene RFC4 35 lower primer related to gene RFC4 36 upper primer related to gene RPL29 37 lower primer related to gene RPL29 38 upper primer related to gene RYBP 39 lower primer related to gene RYBP 40 upper primer related to gene SEC22A 41 lower primer related to gene SEC22A 42 upper primer related to gene SST 43 lower primer related to gene SST 44 upper primer related to gene TFDP2 45 lower primer related to gene TFDP2 46 upper primer related to gene TFG 47 lower primer related to gene TFG 48 upper primer related to gene TRAD 49 lower primer related to gene TRAD 50 sense primer NAU 491 51 primer NAU 483 52 upper ACK1 primer 53 lower ACK1 primer 54 upper MUC4 primer 55 lower MUC4 primer 56 upper STR01 primer 57 lower STR01 primer 58 upper STR02 primer 59 lower STR02 primer 60 SSMUC4_ex4U primer 61 SSMUC4_ex8L primer 62 Muc4_in7u primer 63 Muc4_in7l primer 64 Biotin labelled forward primer flanking the position 1849 SNP 65 reverse primer flanking the position 1849 SNP 66 probe specific for C allele of 1849 SNP 67 Sequence surrounding the XbaI polymorphism. Variant base in XbaI polymorphism is G in the resistant, non-digested, type. 68 Sequence surrounding the XbaI polymorphism. Variant base in XbaI polymorphism is C in the non-resistant, XbaI-digested, type. 69 Upstream primer for the SW2196 microsatellite marker (Alexander et al. (1996) Animal Genetics 27: 137-148) 70 Dovnstream primer for the SW2196 microsatellite marker (Alexander et al. (1996) Animal Genetics 27: 137-148) 71 Upstream primer for the SW207 microsatellite marker (Rohrer et al. (1994) Genetics 136: 231-45). 72 Downstream primer for the SW207 microsatellite marker (Rohrer et al. (1994) Genetics 136: 231-45). 73 Upstream primer for the S0283 microsatellite marker (Davies et al. (1994) Mammalian Genome 5: 707-711). 74 Downstream primer for the S0283 microsatellite marker (Davies et al. (1994) Mammalian Genome 5: 707-711). 75 Upstream primer for the S0075 microsatellite marker (Winterø and Fredholm (1995) Animal Genetics 26: 125-126). 76 Downstream primer for the S0075 microsatellite marker (Winterø and Fredholm (1995) Animal Genetics 26: 125-126). 77 Upstream primer for the SW1876 microsatellite marker (Alexander et al. (1996) Animal Genetics 27: 137-148). 78 Downstream primer for the SW1876 microsatellite marker (Alexander et al. (1996) Animal Genetics 27: 137-148). 79 Upstream primer for the SW225 microsatellite marker (Rohrer et al. (1994) Genetics 136: 231-45). 80 Downstream primer for the SW225 microsatellite marker (Rohrer et al. (1994) Genetics 136: 231-45). 81 Genomic pig DNA showing similarity to the human Mucin 4 gene, exon 1 (GenBank acc. No. AJ000281). 82 Genomic pig DNA showing similarity to the human Mucin 4 gene, exon 1, intron 1, exon 2, intron 2, exon 3, intron 3, exon 4, intron 4, exon 5, intron 5, exon 6 (GenBank acc. Nos. AJ000281, AJ430032, AJ430033, AJ430034) Variation found at position 4847: G in resistant, A in susceptible Variation found at position 4913: G in resistant, T in susceptible Variation found at position 4922: G in resistant, A in susceptible Variation found at position 4926: G in resistant, C in susceptible 83 Genomic pig DNA showing similarity to the human Mucin 4 gene, intron 4, exon 5, intron 5, exon 6, intron 6, exon 7, intron 7, exon 8, intron 8, exon 9, intron, 9, exon 10, intron 10, exon 11, intron 11 (GenBank acc. No. AJ430034). Variation found at position 1659: T in resistant, A in susceptible Variation found at position 1666: G in resistant, T in susceptible Variation found at position 1684: A in resistant, C in susceptible Variation found at position 1726: AACGTG in resistant, 6 bp deletion in susceptible Variation found at position 1740: A in resistant, T in susceptible Variation found at position 1795: T in resistant, C in susceptible Variation found at position 1820: G in resistant, T in susceptible Variation found at position 1912: T in resistant, C in susceptible Variation found at position 2009: T/deletion, not in linkage disequilibrium Variation found at position 2997: A in resistant, G in susceptible Variation found at position 3277: C in resistant, G in susceptible 84 Genomic pig DNA showing similarity to the human Mucin 4 gene, intron 11, exon 12, intron 12 (GenBank acc. No. AJ430034). 85 Genomic pig DNA showing similarity to the human Mucin 4 gene, intron 11, exon 12, intron 12, exon 13, intron 13, exon 14, intron 14 (GenBank acc. No. AJ430034). 86 Genomic pig DNA showing similarity to the human Mucin 4 gene, intron 13, exon 14, intron 14 (GenBank acc. No. AJ430034). 87 Genomic pig DNA showing similarity to the human Mucin 4 gene, intron 14, exon 15, intron 15 (GenBank acc. No. AJ430034). Variation found at position 332 G/A, Not in linkage disequilibrium. 88 Genomic pig DNA showing similarity to the human Mucin 4 gene, intron 15, exon 16, intron 16, exon 17, intron 17, exon 18, intron 18, exon 19, intron 19 (GenBank acc. No. AJ430034).. Variation found at position 3530 G/A, Not in linkage disequilibrium 89 Genomic pig DNA showing similarity to the human Mucin 4 gene, intron 19, exon 20, intron 20, exon 21, intron 21, exon 22, intron 22, exon 23, intron 23 (GenBank acc. No. AJ430034). 90 Genomic pig DNA showing similarity to the human Mucin 4 gene, intron 22, exon 23, intron 23, exon 24, intron 24(GenBank acc. No. AJ430034). 91 Genomic pig DNA showing similarity to the human Mucin 4 gene, exon 25, 3?*** region (GenBank acc. No. AJ430034). 92 contig2 93 contig3 94 contig4 95 contig9 96 contig10 97 contig15 98 contig20 99 contig21 100 contig23 101 contig24 102 contig25 103 contig26 104 contig27 105 contig28 106 contig29 107 contig30 108 contig31 109 contig32 110 contig33 111 contig34 112 contig35 113 contig36 114 contig37 115 contig38 116 contig39 117 contig40 118 contig41 119 contig42 120 contig44 121 contig45 122 contig49 123 contig50 124 contig51 125 contig52 126 contig53 127 contig54 128 contig55 129 contig56 130 contig57 131 contig58 132 contig59 133 contig60 134 contig61 135 contig62 136 contig63 137 contig64 138 contig65 139 contig66 140 contig67 141 contig68 142 contig69 143 contig70 144 contig71 145 contig72 146 contig73 147 contig75 148 contig76 149 contig77 150 contig78 151 contig79 152 contig80 153 contig81 154 contig82 155 contig84 156 contig85 157 contig86 158 contig88 159 contig89 160 contig90 161 contig92 162 contig93 163 contig94 164 contig97 165 contig98 166 contig100 167 contig101 168 contig102 169 contig103 170 contig104 171 contig105 172 contig106 173 contig107 174 contig108 175 contig109 176 contig110 177 contig111 178 contig112 179 contig113 180 contig114 181 contig115 182 contig116 183 contig117 184 contig118 185 contig119 186 contig120 187 contig121 188 contig122 189 contig123 190 contig126 191 contig127 192 contig129 193 contig131 194 contig132 195 40_11.60T7.ab1 196 bac104001a21.g1_A02_02.ab1 197 bac104001b18.g1_H03_15.ab1

1.4 Comparative Mapping

To facilitate the search for the gene responsible for resistance towards E. coli F4ab/F4ac diarrhoea, Is was decided to take advantage of the vast amount of sequence information presented by the sequence of the total human genome.

In order to exploit this information a comparative mapping of the genes on the relevant part of the porcine chromosome 13 (SSC13) and the human chromosome 3 (HSA3) was performed.

DNA from the FISH verified BACs were digested using Sau3AI and the fragments were ligated into the BamHI site of pUC19 and transformed into Epicurian Coli XL1-BLUE cells (Stratagene). The transformants were plated out on LB ampicillin plates and around 100 subclones were picked at random. Plasmid DNA was isolated from the subclones using a Qiaprep spin miniprep kit (Qiagen, Germany). The inserts cloned in the plasmid vectors were sequenced using T3 and T7 primers and BigDye terminator sequencing (Applied Biosystems, Foster City, Calif. USA) and electrophoresed on an ABI377 (Applied Biosystems, Foster City, Calif. USA). The generated sequences were BLASTed against the non-redundant nucleotide database at the NCBI website.

The genes identified in the shot-gun sequencing of the BACs are listed in Table 3.

TABLE 3 Genes identified in the isolated BAC clones. Cyto- genetic position Identified HSA3 Marker BAC id. on Ssc13 genes position Sw207 PigEBAC169o10 q41 KIAA0804 181 Mbp (q28) S0283 PigEBAC177o11 q41 TRAD 121 Mbp (q21.3) S0075 PigEBAC169f15 q41 ADCY5, 120 Mbp (q21.2) SEC22A Sw1876 PigEBAC242a21 na none Sw225 PigEBAC76g23 q44 FLJ22763 106 Mbp (q13)

The human data were taken from the Entrez Genome view build 30 at the NCBI website. Details of the human genes (e.g. TRAD) found in these searches of the DNA sequence database can be found on several Web sites including the NCBI website. Note that SSC13 is the porcine chromosome 13 and that HAS3 is the human chromosome 3.

Based on the matches between the sequences derived from the pig BAC clones and the human genomic sequence a comparative map between SSC13 and HSA3 was drawn, see FIG. 2.

1.5 Comparative Fine Mapping

In order to further improve the comparative map between SSC13 and HSA3, the sequences obtained by shotgun-sequencing that showed similarity to KIAA0804, TRAD and SEC22A were selected. In addition expressed sequence tags (ESTS) predicted to map to SSC13 on the basis of sequence similarity to genes and ESTs known to map to the homologous human chromosome (HSA3) were selected from our resource of porcine small intestine ESTs (Winterø et al., 1996; Winterø & Fredholm, unpublished).

Criteria for selection were that the 5′ cDNA sequences of the respective clones had significant sequence identity (expectation values <e⁻⁶) with the human orthologous genes using BLAST network service against the non-redundant nucleotide database.

Primers were designed in the 3′ UTR region of the selected clones (see Table 4) in order to increase pig specificity. Primer3 (Rozen and Skaletsky, 2000) was used for designing primers. A pig somatic cell hybrid panel (Yerle et al., 1996) and a pig radiation hybrid panel (IMpRH) (Yerle et al., 1998) were used for regional assignment and mapping. PCR conditions were optimized using pig, mouse and hamster genomic DNA. The PCR was performed on 10 ng and 25 ng of DNA from each hybrid line for the somatic and radiation panels, respectively. The PCR conditions were: 0.35 μM of each primer, from 2 to 4 mM of 10 Mg²⁺ and 0.05 units of HotStartTaq (Qiagen, Germany) in a 10 μl reaction volume, during 35 cycles with touch down (TD) 60 or 64. The PCR was performed using 15 min. initial denaturation at 95° C. and subsequently 95° C. for 15 sec. in the additional cycles. Extension was carried out at 72° C. for 1 min. The touchdown was performed by lowering the annealing temperature by 1° C. after each cycle in the first 10 cycles, starting at 64° C. or 60° C. for TD64 and TD60, respectively. The last 25 cycles were performed at annealing temperatures 54° C. or 50° C. for TD64 and TD60, respectively.

The amplification products were resolved in 2% agarose gels and manually scored. The PCR results were directly introduced into the SCH and RH data analysis programs described in Milan et al. (2000). Regional assignment was achieved by using the computer program developed by Chevalet et al. (1997). The results of the radiation hybrid PCR products were analysed with the IMpRH mapping tool developed by Milan et al. (2000). The genes and their localisations are shown in Table 4.

A comparative map between SSC13 and HSA3 using the mapping results from 4 is shown in FIG. 3.

When previously reported comparative data were added (Sun et al. 1999; Van Poucke et al. 1999, Pinton et al. 2000, Van Poucke et al. 2001) to the data generated in this study a comprehensive comparative map between SSC13 and HSA3 was compiled. When zooming in on the candidate region (SCC13q41) it became evident that the candidate regions on HSA3 are q21 and q28-qtel.

1.6 Candidate Genes

When scanning the literature for possible candidate genes for the ETEC F4ab/F4ac status in pigs there have been several reports of proteins associated with susceptibility towards ETEC F4ab/F4ac (Metcalfe et al., 1991; Grange and Mouricout, 1996; Francis et al., 1998; Grange et al., 1998). One report indicates that it is a 74-kDa glycoprotein that belongs to the transferrin family (Grange and Mouricout, 1996), one group suggests glycoproteins of 40 kDa (Metcalfe et al., 1991) and more recent studies points to mucin-type sialoglycoproteins (Francis et al. 1998; Grange et al. 1998). When we considered these reports it became clear that the search for a gene should concentrate on either transferrin-like-genes or mucin-like genes. If the linkage and comparative data was added one gene from the candidate regions of HSA3 became the positional candidate, namely Mucin 4 (MUC4) at Hsa3q29.

TABLE 4 List of genes selected for hybrid cell mapping Human Gene Accession cyto- Pig symbol Clone number genetic cytogenetic PCR primers (E-value) (labid.) (GenBank) position position Upper Lower ADPRTL3 C16b04 AJ508800 3p22.2- 13q21-q22 5′-CCCAGCCATGCTAGGACTAA 5′-AGATTCGCCTCTGAGGTGTC (6e−13) 21.1 (SEQ ID NO: 18) (SEQ ID NO: 19) ARF4 c11f10 AJ508808 3p21.1 13(q21-q22 or 5′-ACCAAAAGCAACATGCAACA 5′-CAGGGAATGCTCCAAAACAC (1e−133) q23-1/2q41) (SEQ ID NO: 20) (SEQ ID NO: 21) ARP c15g08 AJ508798 3p21.1 13(q21-q22 or 5′-TAGTGTAAACCCGCAACAGA 5′-AACAGTTCATCTGTGTCTTC (2e−74) q23-1/2q41) (SEQ ID NO: 22) (SEQ ID NO: 23) DKFZp434- c18g08 AJ508802 3q24 13q23-1/2q41 5′-ACAGCATGAAAAGTGCCTGA 5′-TCCATATCTGTGTCTCATAAA- P0721 (SEQ ID NO: 24) AA (SEQ ID NO: 25) (2e−43) GPX1 c17d11 AJ508799 3p21.3 13(q21-q22 or 5′-TAGTGAGGAACTGTGGTCTG 5′-ATATCGAGCCTGACATCGAA (1e−6) q23-1/2q41) (SEQ ID NO: 26) (SEQ ID NO: 27) KIAA0804 PigEBAC AY156078 3q27 13q41 5′-CTATGTGCCCATGTGCATTC 5′-AACCTGAGAGCATCGGTCAC (3e−49) 169o10 (SEQ ID NO: 28) (SEQ ID NO: 29) KIAA1363 c03b02 AJ508807 3q26.2- 13q23-1/2q41 5′-TCAAGAGGGGCTCAACACTT 5′-TGGAATCATGTACGCAAAGC (1e−64) q27 (SEQ ID NO: 30) (SEQ ID NO: 31) MME c14c07 AJ508801 3q25.1- 13q23-1/2q41 5′-CATATCCACTCCAGGGACAC 5′-ACCAAGACAGTTATGAACCA (2e−77) 25.2 (SEQ ID NO: 32) (SEQ ID NO: 33) RFC4 c18a04 AJ508811 3q27 13(1/2q46-q49) 5′-CGGTGCTTTGGTCATTTTTA 5′-TGCTTAGCTGATGGTGCTGA (7e−30) (SEQ ID NO: 34) (SEQ ID NO: 35) RPL29 c11b05 AJ508797 3q21.3- 13q21-q41 5′-GACAGATCCTGAGGCAGGTT 5′-CAGGTTCTGCCGGCCAAAGT (3e−80) p21.2 (SEQ ID NO: 36) (SEQ ID NO: 37) RYBP c17g07 AJ508795 3p12.3 13q23-1/2q41 5′-AAGCAGAGCAGGTCAATTAAGG 5′-TATTCAGCGGCACAGTAAGC (7e−43) (SEQ ID NO: 38) (SEQ ID NO: 39) SEC22A PigEBAC AY156080 3q21.2 13q41 5′-CCAGCCGGTGTAGTAGACAAG 5′-CCCTTTTAAGGTGTGGAGCTT (2e−60) 169f15 (SEQ ID NO: 40) (SEQ ID NO: 41) SST c09c04 AJ508810 3q28 13(1/2q41 or 5′-TTTGGAGGAGAGGAATTGGA 5′-TGGAGCCTGAAGATTTGTCC (1e−131) 1/2q46-q49) (SEQ ID NO: 42) (SEQ ID NO: 43) TFDP2 c13g02 AJ508806 3q23 13q23-1/2q41 5′-ATAGTAAAACGCGGGTTTGC 5′-GCTGAAGTGGCCTTAGCAAC (3e−83) (SEQ ID NO: 44) (SEQ ID NO: 45) TFG c17b07 AJ508803 3q11-q12 13q42-1/2q46 5′-AGATGACTGAACTTCAACCTAG- 5′-AGCAGCTTCCTAGTTACTTTGG (6e−64) CA (SEQ ID NO: 46) (SEQ ID NO: 47) TRAD PigEBAC AY156082 3q21.3 13q41 5′-CAGGAAGAGCCCCCTAAATC 5′-CAGCAAAGGCAGAAACCTTC (5e−76) I77o11 (SEQ ID NO: 48) (SEQ ID NO: 49)

Example 2 Cloning the Dorcine MUC4 Gene 2.1 Screening Pig BACs containing MUC4

In order to investigate if the MUC4 gene indeed is the gene responsible for resistance towards E. coli ETEC F4ab/F4ac diarrhoea, large portions of the gene were cloned and sequenced.

Plasmid S1325 containing a 3229 bp RACE PCR fragment of the human MUC4 cDNA (Moniaux et al., 1999) was obtained from prof. J.P. Aubert. The fragment was synthetised using total RNA from human colon mucosa. Advantage™ RT-for-PCR kit (Clontech, Heidelberg, Germany) was used to synthesize first-strand cDNA from 1 μg of RNA using the oligo (dT)-anchor primer of the 5′/3′-RACE kit (Boehringer Mannheim, Roche Diagnostics, Meylan, France). Expand long PCR was performed using Expand™ Long Template PCR System (Boehringer Mannheim) with the sense primer NAU 491 (5′-AGCAGGCCGAGTCTTGGATTA-3′, SEQ ID NO:. 50), and as antisense primer the PCR anchor primer of the 5′/3′-RACE kit was used. The PCR amplification reaction mixture (50 μl) contained 5 μl of cDNA, 10 mM sodium dNTPs, 0.4 μM of each primer, 5 μl of 10×Expand™ Long Template PCR buffer 3, 0.75 mM MgC12 and 2.5 units of enzyme mixture. The PCR was performed using a Perkin-Elmer Thermal Cycler Gene Amp® PCR System 9700. PCR parameters were 94° C. for 2 min, followed by 30 cycles at 94° C. for 30 s, annealing at 60° C. for 45 s and elongation at 71° C. for 4 min, of which the 20 last cycles had their elongation time extended by 40 s for each new cycle, followed by a final elongation at 71° C. for 15 min. Nested PCR was carried out using NAU 483 (5′-25 CTGTTTCTCTACCAGAGCGGT-3′, SEQ ID NO:. 51) and the PCR anchor primer. The amplified product was electrophoresed on 1% TBE (1 ×TBE=45 mM Tris/borate/1 mM EDTA) agarose gel and stained with ethidium bromide. The band was cut out, purified using QIAquick Gel Extraction Kit (Qiagen), and subcloned into the Original TA Cloning® Kit (Invitrogen, Leek, The Netherlands). The insert was purified and randomly labelled using 32P-dCTP.

High density gridded filters of a Pig BAC library (Anderson et al., 2000) provided by UK HGMP Resource Centre was hybridised with the human MUC4 probe.

Four positive BAC clones were selected and these are listed in Table 5.

TABLE 5 Mucin 4 positive Pig EBAC clones Clone name PigEBAC53f14 PigEBAC104b01 PigEBAC222b07 PigEBAC250f16

2.2 Contig of MUC4 Pig E BAC clones

The ends of the four MUC4 pig E BAC clones along with subclones from each of the four MUC4 pig E BAC clones were sequenced using BigDye terminator chemistry and sequence tagged sites (STSS) were derived. The STSs are listed in Table 6.

TABLE 6 STSs used for BAC contig SEQ SEQ ID ID Name Upper primer NO: Lower primer NO: ACK1 5′-CGTGACGACCTCAACGTTAC 52 5′-CTGCCGATCTTCAGGTC 53 MUC4 5′-CTACTCCAACCCTCCCCTCA 54 5′-GAAATCAGCATCATCCCAGAA 55 STR01 5′-CACACATGTTCATACAGTGCTGA 56 5′-CCAGGCACTTCTGGCTCTTA 57 STR02 5′-CAATGTGCCAATTTCCACTG 58 5′-ATACGGGGAGTTTGGGGTTA 59

This allowed a partial determination of how the BAC clones overlap. The contig is shown in FIG. 4.

From the BAC end sequence it was shown that PigEBAC250f16 contained a 5′-truncation of the MUC4 gene. PigEBACs 53f14 and 222b07 contained a gene upstream to MUC4, namely ACK1 and thus these clones are good candidates for containing the entire pig genomic MUC4 sequence. Due to its the smaller size clone 222b07 was selected for further sequencing.

2.3 Shotgun Sequencing of PigEBAC222b07

BAC DNA was prepared using the Qiagen Large-construct kit (Qiagen, Germany) and the BAC DNA was subcloned using the TOPO shotgun subcloning kit (Invitrogen, Calif., USA). Clones were plated on LB ampicillin plates and 1536 clones were picked into four 384-well plates. Plasmid preparations were performed using Qiaprep spin miniprep kit (Qiagen, Germany). The inserts were sequenced using T3 and T7 primers and BigDye terminator sequencing (Applied Biosystems, Foster City, Calif., USA) and electrophoresed on an ABI3100 (Applied Biosystems, Foster City, Calif., USA).

The generated tracefiles were base called and quality checked using PHRED (Ewing et al., 1998), vector sequences were masked out using CROSS MATCH, sequences were assembled into contigs using PHRAP and viewed using CONSED (Gordon et al. 1998). All generated sequences (ie. contigs and singlet) The sequences were BLAST-searched against the non-redundant nucleotide database at the NCBI website. In addition FASTA33 searches using the human MUC4 genomic sequences (GenBank accession AJ430032, AJ430033, AJ430034) was performed.

Around 1200 subclones have been sequenced and sequences from all 25 exons of the porcine MUC4 have been identified by comparison of the pig sequences with the sequence of the human MUC4 gene. We have full sequence information from all exons except exons 1 and 25. Further, we have sequence information on all introns, and we have full information except from introns 1, 11, 14, 16, 19 and 24 (See Table 2, “Sequences related to the invention”).

Example 3 Identifying Polymorphisms in the MUC4 Gene Linked to Resistance towards E. coli ETEC F4ab/F4ac Diarrhoea

To identify possible genetic variations in the porcine MUC4 gene that links to resistance towards E. coli ETEC F4ab/F4ac diarrhoea the sequence information obtained in example 2 was exploited as described.

After having generated the sequences of exons 4 and 8 the following PCR primers were designed:

SSMUC4_ex4U: 5′-GAC TTC ACC TCG CCA CTC TT (SEQ ID NO:. 60) SSMUC4_ex8L: 5′-CGA TAC TTC TCC CAC ACT GG (SEQ ID NO:. 61)

Using these primers on pig genomic DNA we generated an approximately 4 kb long range PCR product using Elongase (Invitrogen, Calif., USA). Initial denaturation was 94° C. for 2 min and 35 cycles 94° C. 30 s, 60° C. 1 min, 68° C. 10 min. After amplification different restriction enzymes were tested on amplified fragments from animals with known F4ab/F4ac genotype and a XbaI polymorphism was discovered.

3.1 Linkage Analysis with MUC4

The pedigree used in the linkage analysis was genotyped for the XbaI polymorphism and complete co-segregation with the F4ab/F4ac was shown. Multi-point analysis firmly localised MUC4 to the interval between Sw207 and S0075, showing no recombination with the F4ab/F4ac locus.

3.2 Linkage Disequilibrium

In the 10 parental animals of the linkage mapping pedigree 18 chromosomes have known F4ab/F4ac status (ie. The chromosomal region is known to be either susceptible or resistant). The haplotypes surrounding the F4ab/F4ac locus show maximal linkage disequilibrium with MUC4. The probability of such observation using Fisher's exact test is P=0.00005. None of the other markers in the region are showing the same degree of linkage disequilibrium.

3.3 RT-PCR

Complementary DNA was synthesised from RNA isolated from mucosal tissue of jejunum, ileum and colon. The SSMUC4_ex4U/SSMUC4_ex8L primers were used in PCR on 5 ng of cDNA from the different tissues in a total volume of 20:1 using 1×PCR buffer, 200:M of each dNTP, 0.4:M of each primer and 0.25 units HotStarTaq (Qiagen, USA).

Thermocycling was performed using 15 min initial denaturation at 95° C. and subsequently 95° C. for 15 s in the additional cycles. Extension was carried out at 72° C. for 1 min. Touchdown was performed lowering the annealing temperature by 1° C. after each cycle in the first 10 cycles, starting at 60° C. The last 25 cycles were performed at annealing temperature 50° C.

Electrophoresis in 2% agarose gel revealed a RT-PCR product of around 600 bp in all three tissues.

The result clearly showed that Mucin 4 was expressed in jejunum, ileum and colon in pigs.

3.5 Characterisation of the XbaI-Polymorphism

By using PCR and sequencing of PCR products, genomic sequences were generated of pigs with known F4ab/F4ac genotypes from the used pedigree. Seventeen polymorphisms in the genomic sequence of the MUC4-gene were found. In the region exon 5 to exon 8 two MUC4-haplotypes, which differ by at least 14 single nucleotide substitutions and a 6 bp deletion, can be described. One of these haplotypes is consistent with the resistance allele towards E. coli F4ab/F4ac diarrhoea and the other haplotype with the susceptibility towards E. coli F4ab/F4ac diarrhoea in our family material. In FIG. 5. the current sequencing status is shown using the genomic organisation of the human MUC4 as a scaffold.

In Tables 7A-D the differences between the two haplotypes are shown.

TABLE 7A Positions of polymorphisms. The positions are related to the two sequences of SEQ ID NO: 6 and SEQ ID NO: 8. The polymorphisms of SEQ ID NO: 6 are present in a part of the sequence that shows similarity of intron 5 of the human MUC4 gene. The polymorphisms of SEQ ID NO: 8 are present in a part of the sequence that shows similarity of intron 7 of the human MUC4 gene. Sequence SEQ SEQ ID NO: 6 ID NO: 8 Position in sequence 1059 1125 1134 1138 1849 2129 Resistant G G G G G T haplotype Susceptible A T A C C C haplotype

TABLE 7B Positions of polymorphisms. The positions are related to the sequences of SEQ ID NO: 82. The polymorphisms are present in a part of SEQ ID NO: 82 that shows similarity of intron 5 of the human MUC4 gene. Sequence SEQ ID NO 82 Position in sequence 4847 4913 4922 4926 Resistant haplotype G G G G Susceptible haplotype A T A C

TABLE 7C Positions of polymorphisms. The positions are related to the sequences of SEQ ID NO: 83. The polymorphisms are present in a part of SEQ ID NO: 83 that shows similarity of intron 6 of the human MUC4 gene. Sequence SEQ ID NO: 83 Position in sequence 1659 1666 1684 1726 1740 1795 1820 1912 2009 Resistant T G A AACGTG A T G T T/deletion haplotype not in linkage Susceptible A T C deletion T C T C disequilibrium haplotype

TABLE 7D Positions of polymorphisms. The positions are related to the sequences of SEQ ID NO:s 83, 87 and 88. The two polymorphisms of SEQ ID NO: 83 are present in a part of the sequence that shows similarity of intron 7 of the human MUC4 gene. Accordingly, the polymorphisms of SEQ ID NO: 87 and 88 are present in parts of the sequences related to intron 15 and Exon 18, respectively. Sequence/SEQ ID NO: Intron 7/ SEQ ID NO: Intron 15/ Exon 18/ 83 SEQ ID NO: 87 SEQ ID NO: 88 Position in sequence 2997 3277 332 3530 Resistant A C G/A not in linkage G/A not in linkage haplotype disequilibrium disequilibrium Susceptible G G haplotype

EXAMPLE 4 DNA-Based Assays that Discriminate between the Resistant and Susceptible Alleles in the MUC4-Gene

In order to facilitate the validation of the MUC4 polymorphism different tests to discriminate between the resistant and susceptible alleles in the MUC4-gene were developed. The first SNP discovered was at the 1849 position in sequence #8 (intron 7). This SNP results in an XbaI restrictionsite in the resistant allele. The SNP was discovered using long-range PCR-RFLP (see Example 3) and after further characterisation a simple PCR-based test to allow more rapid genotyping was developed. Furthermore, a Dynamic allele-specific hybridisation assay to allow genotyping of crude DNA preparations was developed. The consensus sequence around the position 1849 SNP is shown in FIGS. 6 and 7.

4.1 PCR-RFLP

In the PCR-RFLP assay we performed PCR on 25 ng genomic DNA from pig in a total volume of 20:1 using 1×PCR buffer, 200:M of each dNTP, 0.4:M of each primer and 0.25 units HotStarTaq (Qiagen, USA). The primer sequences are as follows:

Muc4_in7u: 5′-GTG CCT TGG GTG AGA GGT TA-3′ (SEQ ID NO:. 62) Muc4_in7l: 5′-CAC TCT GCC GTT CTC TTT CC-3′ (SEQ ID NO:. 63)

Thermocycling was performed using 15 min initial denaturation at 95° C. and subsequently 95° C. for 15 s in the additional cycles. Extension was carried out at 72° C. for 1 min. Touchdown was performed lowering the annealing temperature by 1° C. after each cycle in the first 10 cycles, starting at 60° C. The last 25 cycles were performed at annealing temperature 50° C. The PCR product obtained from pig genomic DNA is 367 bp and 10 μl of the PCR product is used for XbaI digest as recommended by the supplier (New England Biolabs, Mass., USA). After digest with XbaI the fragments are:

Resistant allele 367 bp Susceptible allele 151 bp, 216 bp

The following patterns are observed from the three different genotypes:

Resistant 367 bp Susceptible heterozygote 151 bp, 216 bp, 367 bp Susceptible homozygote 151 bp, 216 bp

4.2 Dynamic Allele-Specific Hybridisation (DASH) Assay

DASH was carried out as described in Howell et al. (1999) and by the use of primers flanking the position 1849 SNP, the conditions were as follows:

Biotin labelled forward primer: (SEQ ID NO:. 64) 5′-biotin-GGCAATGACTTATCTATTTGTACC-3′ Reverse primer: (SEQ ID NO:. 65) 5′-GTATATTACAACAACCCCATGAAGG-3′ Probe specific for the C allele: (SEQ ID NO:. 66) 5′-CCATTCTAGAGATACAG-3′

PCR was performed in 20 μl using the following reagents:

Water 13.52 μl MgCl₂ (25 mM) 0.80 μl 10 × PCR buffer 2.00 μl Biotin-labelled forward primer (2.5 pmol/μl) 0.80 μl Non-labelled revers primer (15 pmol/μl) 0.80 μl Taq polymerase (5 units/μl) 0.08 μl DNA (10-25 ng/μl) 1.00 μl dNTP mix (4 mM each) 1.00 μl Total 20.00 μl

Thermocycling was performed using 15 min initial denaturation at 95° C. and subsequently 95° C. for 15 s in the additional cycles. Extension is carried out at 72° C. for 1 min. Touchdown was performed lowering the annealing temperature by 1° C. after each cycle in the first 10 cycles, starting at 60° C. The last 25 cycles were performed at annealing temperature 50° C.

After PCR 10 μl of HEN buffer (0.1 M HEPES, 50 mM NaCl, 10 mM EDTA pH=8.0) and 10 μl of PCR product were added to each well of a streptavidin coated microtiter plate and incubated for 16 hours at +4° C. The PCR mixture was removed and 50 μl of 0.1 M NaOH was added and incubated for 1-5 min. and removed. The plate was then washed with 50 μl of HEN buffer. DASH buffer (1 μl SybrGreen (Molecular Probes, Oreg., USA) in 10 ml HEN buffer) (49 μl) and 1 μl of the allele specific probe (30 pmol/μl) was added to each well. Samples was heated to 85° C. and let to cool down to between 20° C. and 25° C. in less than 10 min. Samples was washed with 50 μl HEN buffer and 50 μl DASH buffer was added. DASH was performed using heat rate set at 0.03 and heat range 35° C. to 90° C.

4.3 Validation

The tests were verified on the pig pedigree material and as described previously that maximal linkage disequilibrium between F4ab/F4ac and MUC4 were found. In addition 13 unrelated pigs were tested with score 4 (i.e. strong adhesion) in the adhesion test and they all had at least one copy of the susceptible haplotype. Twenty piglets with E. coli O149, F4ac diarrhoea have also been genotyped in the MUC4 locus and all carried the susceptible haplotype. Nine resistant animals were tested and all animals showed either no or weak adhesion. In order to test previous report that the Chinese pig breed Meishan is resistant two sows were tested and both were shown to be homozygous for the resistant haplotype.

Example 5 Population Studies

The long range PCR-RFLP test was used in a limited number of animals from the four main commercial breeds in Denmark. The estimated frequencies of the E. coli F4ab/F4ac susceptibility allele are shown in Table 8.

TABLE 8 Frequencies of the position 1849 C allele (ETEC F4ab/F4ac susceptible) No. Animals f(pos 1849 C) Duroc 17 0.06 Hampshire 9 0.00 Landrace 14 0.96 Yorkshire 19 0.58 Total 59 0.44

Conclusion

The F4ab/F4ac locus has been firmly positioned by linkage analysis and Mucin 4 was a strong positional candidate gene. Expression analysis by the use of RT-PCR clearly showed that MUC4 is expressed in intestinal mucosa in the pig. Polymorphisms in introns 5 and 7 of Mucin 4 have been discovered and two haplotypes of the gene are presented. The difference between the two haplotypes shows at least 14 substitutions and this indicate haplotypes with different origins, ie. Asian and European. The two founder wild boars in the family material are homozygous resistant for ETEC F4ab/F4ac and they share the same haplotype for the MUC4-gene. Two of the Yorkshire sows were heterozygous ETEC F4ab/F4ac susceptible and these two sows had both the resistant and susceptible haplotypes. The remaining Yorkshire sows were homozygous and all had the same haplotype of the MUC4-gene. Sequencing of unrelated commercial pigs has not contributed extra haplotypes. Genotyping of Chinese Meishan pigs was in agreement with this breed being resistant towards E. coli F4ab/F4ac.

Example 6 Identification of New Genetic Polymorphisms

Given the technical means that are provided with the present invention new genetic polymorphisms are easily identified by the following procedure.

Shot-gun sequencing is continued and the entire PigEBAC222b07 is assembled into one contig. The entire genomic sequence of porcine Mucin 4 will be revealed and PCR primers flanking each of the 25 exons is designed. The 25 exons are sequenced in animals with the different Mucin 4 genotypes. Comparisons of the exon sequences will reveal coding SNPs and these is tested in the pedigree used for linkage mapping and in additional unrelated animals.

Regions flanking the Mucin 4 gene will also be sequenced and SNPs in these region is tested for linkage disequilibrium.

The region showing maximal linkage disequilibrium will be characterised using SNPs flanking the Mucin 4 region on pig chromosome 13.

Real time RT-PCR will be used to evaluate MUC4 expression profiles in all three different Mucin 4 haplotypes.

Transfection studies and the use of transgenic animals using different porcine Mucin 4 gene variants will be used to prove the association between Mucin 4 variants and ETEC F4ab/F4ac status.

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1. A method for identifying if a pig is resistant or non-resistant to an E. coli pathogen carrying fimbriae F4ac or F4 ab, the method comprising i) obtaining a sample from said pig, said sample comprising genomic material, ii) detecting in said genetic material the genotype of alleles of a genetic polymorphism indicative of resistance or susceptibility to said E. coli pathogen; iii) determining that said pig is resistant to said E. coli pathogen if the pig is homozygous for an allele of the genetic polymorphism indicative of resistance to ETEC; iv) determining that said pig is non-resistant to said E. coli pathogen and a non-carrier of resistance to said E. coli pathogen if the pig is homozygous for an allele of the genetic polymorphism indicative of non-resistance to said E. coli pathogen; and v) determining that said pig is non-resistant to said E. coli pathogen and a carrier of resistance to said E. coli pathogen if the pig is heterozygous and contains both an allele of the genetic polymorphism indicative of resistance to ETEC and an allele of the genetic polymorphism indiciative of non-resistance to said E. coli pathogen, wherein the allele of a genetic polymorphism indicative of resistance to ETEC is selected from the group consisting of: G at position 1849 of SEQ ID NO: 8; T at position 2129 of SEQ ID NO: 8; A at position 2997 of SEQ ID NO: 83; and C at position 3277 of SEQ ID NO: 83, and wherein the allele of a genetic polymorphism indicative of non-resistance to ETEC is selected from the group consisting of: C at position 1849 of SEQ ID NO: 8; C at position 2129 of SEQ ID NO: 8; G at position 2997 of SEQ ID NO: 83; and G at position 3277 of SEQ ID NO:
 83. 2. A method according to claim 1, wherein the pig is selected from the group of pigs consisting of sus scrota (Suidae), Yorkshire, Danish Yorkshire, Danish Duroc, Landrace, Danish Landrace, White Danish Landrace, Blackspotted Danish Landrace, Hampshire, Danish Hampshire, Poland China, Hereford and any cross-breedings thereof.
 3. A method according to claim 1, wherein the pig is selected from the group consisting of a boar, a sow, a suckling piglet, a weaned pig, a grower pig and a finisher pig.
 4. A method according to claim 1, wherein the sample is selected from the group consisting of a material comprising DNA and/or RNA, blood, saliva, tissue, throat swap, semen, and combinations thereof.
 5. The method according to claim 1, wherein the steps of determining if the pig is resistant, non-resistant, or a non-resistant carrier of resistance to said E. coli pathogen can be performed using a technique selected from the group consisting of allele specific PCR, mini sequencing, primer extension, pyro-sequencing, PCR-RFLP, allele-specific rolling circle amplification, ARMS (Amplification Refracting Mutation System), hybridisation e.g. to DNA arrays, DASH (Dynamic Allele-Specific Hybridisation), melting curve measurement, primer extension followed by MALDI-TOF mass spectrometry and any combinations thereof.
 6. A method according to claim 1, further comprising at least one of the following steps: (i) extracting genomic DNA from said sample; (ii) amplifying at least a fragment of extracted genomic DNA to obtain an amplification product; (iii) contacting an amplification product with a restriction enzyme; (iv) separating restriction fragments by gel electrophoresis; (v) determining number and lengths of restriction fragments; and (vi) detecting the presence of a polymorphism based on number and lengths of restriction fragments.
 7. The method according to claim 6, wherein the restriction enzyme is XbaI.
 8. A method for breeding pigs that are resistant to ETEC, the method comprising: (i) determining that a first pig is resistant to ETEC using the method according to claim 1; (ii) selecting said first pig; and (iii) breeding said first pig with a second pig to obtain progeny that is more likely to be resistant to ETEC than progeny from randomly chosen parent pigs.
 9. A method for breeding pigs that are resistant to ETEC, the method comprising: (i) determining that a first pig is resistant to ETEC using the method according to claim 1; (ii) selecting said first pig; (iii) determining that a second pig is resistant to ETEC using the method according to claim 1; (iV) breeding said first pig with said second pig to obtain progeny that is more likely to be resistant to ETEC than progeny from randomly chosen parent pigs.
 10. A method for producing pork meat, comprising the steps of: (i) obtaining pig progeny according to the method of claim 8 or claim 9; and (ii) preparing pork meat from the pig progeny. 